From 10c1de88436bba405cbeb803c8b54e002a4ab7da Mon Sep 17 00:00:00 2001
From: Carlos Gutierrez <cargdev@gmail.com>
Date: Fri, 16 Jan 2026 11:52:46 -0500
Subject: [PATCH] Refactor: Restructure project into core, features, adapters,
 and config modules

---
 .../{ => adapters/nvim}/autocmds.lua          |  32 ++---
 .../nvim/cmp}/init.lua                        |   0
 .../{ => adapters/nvim}/commands.lua          | 136 +++++++++---------
 .../ui.lua => adapters/nvim/ui/chat.lua}      |  10 +-
 .../nvim/ui}/context_modal.lua                |   2 +-
 .../nvim/ui}/diff_review.lua                  |   2 +-
 .../{agent => adapters/nvim/ui}/logs.lua      |   0
 .../{ => adapters/nvim/ui}/logs_panel.lua     |   4 +-
 .../nvim/ui/switcher.lua}                     |   4 +-
 .../{window.lua => adapters/nvim/windows.lua} |   4 +-
 lua/codetyper/{ => config}/credentials.lua    |   2 +-
 .../{config.lua => config/defaults.lua}       |   0
 lua/codetyper/{ => config}/preferences.lua    |   2 +-
 .../{cost.lua => core/cost/init.lua}          |   2 +-
 .../{agent => core/diff}/conflict.lua         |   6 +-
 lua/codetyper/{agent => core/diff}/diff.lua   |   2 +-
 lua/codetyper/{agent => core/diff}/patch.lua  |  40 +++---
 .../{agent => core/diff}/search_replace.lua   |   0
 .../{agent => core/events}/queue.lua          |   2 +-
 .../intent.lua => core/intent/init.lua}       |   0
 .../{agent => core/llm}/confidence.lua        |   2 +-
 lua/codetyper/{ => core}/llm/copilot.lua      |  14 +-
 lua/codetyper/{ => core}/llm/gemini.lua       |  10 +-
 lua/codetyper/{ => core}/llm/init.lua         |  18 +--
 lua/codetyper/{ => core}/llm/ollama.lua       |  12 +-
 lua/codetyper/{ => core}/llm/openai.lua       |  12 +-
 lua/codetyper/{agent => core/llm}/parser.lua  |   0
 lua/codetyper/{ => core}/llm/selector.lua     |  10 +-
 .../{brain => core/memory}/delta/commit.lua   |   8 +-
 .../{brain => core/memory}/delta/diff.lua     |   2 +-
 .../{brain => core/memory}/delta/init.lua     |  28 ++--
 .../{brain => core/memory}/graph/edge.lua     |   6 +-
 .../{brain => core/memory}/graph/init.lua     |  10 +-
 .../{brain => core/memory}/graph/node.lua     |   6 +-
 .../{brain => core/memory}/graph/query.lua    |   8 +-
 lua/codetyper/{brain => core/memory}/hash.lua |   0
 lua/codetyper/{brain => core/memory}/init.lua |  18 +--
 .../memory}/learners/convention.lua           |   2 +-
 .../memory}/learners/correction.lua           |   2 +-
 .../{brain => core/memory}/learners/init.lua  |  14 +-
 .../memory}/learners/pattern.lua              |   2 +-
 .../memory}/output/formatter.lua              |   2 +-
 .../{brain => core/memory}/output/init.lua    |   8 +-
 .../{brain => core/memory}/storage.lua        |   4 +-
 .../{brain => core/memory}/types.lua          |   0
 .../{agent => core/scheduler}/executor.lua    |   4 +-
 .../{agent => core/scheduler}/loop.lua        |   8 +-
 .../{agent => core/scheduler}/resume.lua      |   2 +-
 .../{agent => core/scheduler}/scheduler.lua   |  34 ++---
 .../{agent => core/scheduler}/worker.lua      |  26 ++--
 .../{agent/scope.lua => core/scope/init.lua}  |   0
 lua/codetyper/{agent => core}/tools/base.lua  |   0
 lua/codetyper/{agent => core}/tools/bash.lua  |   2 +-
 lua/codetyper/{agent => core}/tools/edit.lua  |   2 +-
 lua/codetyper/{agent => core}/tools/glob.lua  |   2 +-
 lua/codetyper/{agent => core}/tools/grep.lua  |   2 +-
 .../{agent/tools.lua => core/tools/init.lua}  |   0
 .../init.lua => core/tools/registry.lua}      |  12 +-
 lua/codetyper/{agent => core}/tools/view.lua  |   2 +-
 lua/codetyper/{agent => core}/tools/write.lua |   2 +-
 .../agents}/context_builder.lua               |   2 +-
 .../agents/engine.lua}                        |  16 +--
 .../{agent => features/agents}/init.lua       |  20 +--
 .../{agent => features/agents}/linter.lua     |  12 +-
 .../agents}/permissions.lua                   |   0
 .../{ask.lua => features/ask/engine.lua}      |   6 +-
 lua/codetyper/{ => features}/ask/explorer.lua |   2 +-
 lua/codetyper/{ => features}/ask/intent.lua   |   0
 .../{agent => features/completion}/inject.lua |   2 +-
 .../completion/inline.lua}                    |   2 +-
 .../completion/suggestion.lua}                |   0
 .../{ => features}/indexer/analyzer.lua       |   4 +-
 lua/codetyper/{ => features}/indexer/init.lua |  16 +--
 .../{ => features}/indexer/memory.lua         |   2 +-
 .../{ => features}/indexer/scanner.lua        |   2 +-
 lua/codetyper/init.lua                        |  24 ++--
 lua/codetyper/inject.lua                      |   6 +-
 lua/codetyper/parser.lua                      |   2 +-
 lua/codetyper/{ => support}/gitignore.lua     |   2 +-
 lua/codetyper/{ => support}/health.lua        |   6 +-
 lua/codetyper/{utils => support}/langmap.lua  |   0
 lua/codetyper/{ => support}/tree.lua          |   2 +-
 lua/codetyper/{ => support}/utils.lua         |   0
 83 files changed, 337 insertions(+), 337 deletions(-)
 rename lua/codetyper/{ => adapters/nvim}/autocmds.lua (98%)
 rename lua/codetyper/{cmp_source => adapters/nvim/cmp}/init.lua (100%)
 rename lua/codetyper/{ => adapters/nvim}/commands.lua (92%)
 rename lua/codetyper/{agent/ui.lua => adapters/nvim/ui/chat.lua} (99%)
 rename lua/codetyper/{agent => adapters/nvim/ui}/context_modal.lua (99%)
 rename lua/codetyper/{agent => adapters/nvim/ui}/diff_review.lua (99%)
 rename lua/codetyper/{agent => adapters/nvim/ui}/logs.lua (100%)
 rename lua/codetyper/{ => adapters/nvim/ui}/logs_panel.lua (99%)
 rename lua/codetyper/{chat_switcher.lua => adapters/nvim/ui/switcher.lua} (88%)
 rename lua/codetyper/{window.lua => adapters/nvim/windows.lua} (97%)
 rename lua/codetyper/{ => config}/credentials.lua (99%)
 rename lua/codetyper/{config.lua => config/defaults.lua} (100%)
 rename lua/codetyper/{ => config}/preferences.lua (99%)
 rename lua/codetyper/{cost.lua => core/cost/init.lua} (99%)
 rename lua/codetyper/{agent => core/diff}/conflict.lua (99%)
 rename lua/codetyper/{agent => core/diff}/diff.lua (99%)
 rename lua/codetyper/{agent => core/diff}/patch.lua (96%)
 rename lua/codetyper/{agent => core/diff}/search_replace.lua (100%)
 rename lua/codetyper/{agent => core/events}/queue.lua (99%)
 rename lua/codetyper/{agent/intent.lua => core/intent/init.lua} (100%)
 rename lua/codetyper/{agent => core/llm}/confidence.lua (98%)
 rename lua/codetyper/{ => core}/llm/copilot.lua (98%)
 rename lua/codetyper/{ => core}/llm/gemini.lua (97%)
 rename lua/codetyper/{ => core}/llm/init.lua (93%)
 rename lua/codetyper/{ => core}/llm/ollama.lua (97%)
 rename lua/codetyper/{ => core}/llm/openai.lua (97%)
 rename lua/codetyper/{agent => core/llm}/parser.lua (100%)
 rename lua/codetyper/{ => core}/llm/selector.lua (98%)
 rename lua/codetyper/{brain => core/memory}/delta/commit.lua (96%)
 rename lua/codetyper/{brain => core/memory}/delta/diff.lua (99%)
 rename lua/codetyper/{brain => core/memory}/delta/init.lua (87%)
 rename lua/codetyper/{brain => core/memory}/graph/edge.lua (98%)
 rename lua/codetyper/{brain => core/memory}/graph/init.lua (94%)
 rename lua/codetyper/{brain => core/memory}/graph/node.lua (98%)
 rename lua/codetyper/{brain => core/memory}/graph/query.lua (98%)
 rename lua/codetyper/{brain => core/memory}/hash.lua (100%)
 rename lua/codetyper/{brain => core/memory}/init.lua (91%)
 rename lua/codetyper/{brain => core/memory}/learners/convention.lua (99%)
 rename lua/codetyper/{brain => core/memory}/learners/correction.lua (99%)
 rename lua/codetyper/{brain => core/memory}/learners/init.lua (93%)
 rename lua/codetyper/{brain => core/memory}/learners/pattern.lua (98%)
 rename lua/codetyper/{brain => core/memory}/output/formatter.lua (99%)
 rename lua/codetyper/{brain => core/memory}/output/init.lua (94%)
 rename lua/codetyper/{brain => core/memory}/storage.lua (98%)
 rename lua/codetyper/{brain => core/memory}/types.lua (100%)
 rename lua/codetyper/{agent => core/scheduler}/executor.lua (99%)
 rename lua/codetyper/{agent => core/scheduler}/loop.lua (97%)
 rename lua/codetyper/{agent => core/scheduler}/resume.lua (98%)
 rename lua/codetyper/{agent => core/scheduler}/scheduler.lua (95%)
 rename lua/codetyper/{agent => core/scheduler}/worker.lua (97%)
 rename lua/codetyper/{agent/scope.lua => core/scope/init.lua} (100%)
 rename lua/codetyper/{agent => core}/tools/base.lua (100%)
 rename lua/codetyper/{agent => core}/tools/bash.lua (98%)
 rename lua/codetyper/{agent => core}/tools/edit.lua (99%)
 rename lua/codetyper/{agent => core}/tools/glob.lua (98%)
 rename lua/codetyper/{agent => core}/tools/grep.lua (97%)
 rename lua/codetyper/{agent/tools.lua => core/tools/init.lua} (100%)
 rename lua/codetyper/{agent/tools/init.lua => core/tools/registry.lua} (95%)
 rename lua/codetyper/{agent => core}/tools/view.lua (98%)
 rename lua/codetyper/{agent => core}/tools/write.lua (96%)
 rename lua/codetyper/{agent => features/agents}/context_builder.lua (99%)
 rename lua/codetyper/{agent/agentic.lua => features/agents/engine.lua} (97%)
 rename lua/codetyper/{agent => features/agents}/init.lua (96%)
 rename lua/codetyper/{agent => features/agents}/linter.lua (96%)
 rename lua/codetyper/{agent => features/agents}/permissions.lua (100%)
 rename lua/codetyper/{ask.lua => features/ask/engine.lua} (99%)
 rename lua/codetyper/{ => features}/ask/explorer.lua (99%)
 rename lua/codetyper/{ => features}/ask/intent.lua (100%)
 rename lua/codetyper/{agent => features/completion}/inject.lua (99%)
 rename lua/codetyper/{completion.lua => features/completion/inline.lua} (99%)
 rename lua/codetyper/{suggestion/init.lua => features/completion/suggestion.lua} (100%)
 rename lua/codetyper/{ => features}/indexer/analyzer.lua (99%)
 rename lua/codetyper/{ => features}/indexer/init.lua (96%)
 rename lua/codetyper/{ => features}/indexer/memory.lua (99%)
 rename lua/codetyper/{ => features}/indexer/scanner.lua (99%)
 rename lua/codetyper/{ => support}/gitignore.lua (99%)
 rename lua/codetyper/{ => support}/health.lua (92%)
 rename lua/codetyper/{utils => support}/langmap.lua (100%)
 rename lua/codetyper/{ => support}/tree.lua (99%)
 rename lua/codetyper/{ => support}/utils.lua (100%)

diff --git a/lua/codetyper/autocmds.lua b/lua/codetyper/adapters/nvim/autocmds.lua
similarity index 98%
rename from lua/codetyper/autocmds.lua
rename to lua/codetyper/adapters/nvim/autocmds.lua
index b39f36c..676fd1d 100644
--- a/lua/codetyper/autocmds.lua
+++ b/lua/codetyper/adapters/nvim/autocmds.lua
@@ -2,7 +2,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Autocommand group name
 local AUGROUP = "Codetyper"
@@ -43,7 +43,7 @@ local function schedule_tree_update()
 	end
 
 	tree_update_timer = vim.defer_fn(function()
-		local tree = require("codetyper.tree")
+		local tree = require("codetyper.support.tree")
 		tree.update_tree_log()
 		tree_update_timer = nil
 	end, TREE_UPDATE_DEBOUNCE_MS)
@@ -179,7 +179,7 @@ function M.setup()
 		group = group,
 		pattern = "*.coder.*",
 		callback = function(ev)
-			local window = require("codetyper.window")
+			local window = require("codetyper.adapters.nvim.windows")
 			if window.is_open() then
 				window.close_split()
 			end
@@ -397,11 +397,11 @@ function M.check_for_closed_prompt()
 			if scheduler_enabled then
 				-- Event-driven: emit to queue
 				vim.schedule(function()
-					local queue = require("codetyper.agent.queue")
-					local patch_mod = require("codetyper.agent.patch")
-					local intent_mod = require("codetyper.agent.intent")
-					local scope_mod = require("codetyper.agent.scope")
-					local logs_panel = require("codetyper.logs_panel")
+					local queue = require("codetyper.core.events.queue")
+					local patch_mod = require("codetyper.core.diff.patch")
+					local intent_mod = require("codetyper.core.intent")
+					local scope_mod = require("codetyper.core.scope")
+					local logs_panel = require("codetyper.adapters.nvim.ui.logs_panel")
 
 					-- Open logs panel to show progress
 					logs_panel.ensure_open()
@@ -543,7 +543,7 @@ end
 ---@param skip_processed_check? boolean Skip the processed check (for manual mode)
 function M.process_single_prompt(bufnr, prompt, current_file, skip_processed_check)
 	local parser = require("codetyper.parser")
-	local scheduler = require("codetyper.agent.scheduler")
+	local scheduler = require("codetyper.core.scheduler.scheduler")
 
 	if not prompt.content or prompt.content == "" then
 		return
@@ -567,11 +567,11 @@ function M.process_single_prompt(bufnr, prompt, current_file, skip_processed_che
 
 	-- Process this prompt
 	vim.schedule(function()
-		local queue = require("codetyper.agent.queue")
-		local patch_mod = require("codetyper.agent.patch")
-		local intent_mod = require("codetyper.agent.intent")
-		local scope_mod = require("codetyper.agent.scope")
-		local logs_panel = require("codetyper.logs_panel")
+		local queue = require("codetyper.core.events.queue")
+		local patch_mod = require("codetyper.core.diff.patch")
+		local intent_mod = require("codetyper.core.intent")
+		local scope_mod = require("codetyper.core.scope")
+		local logs_panel = require("codetyper.adapters.nvim.ui.logs_panel")
 
 		-- Open logs panel to show progress
 		logs_panel.ensure_open()
@@ -840,7 +840,7 @@ local auto_opened_buffers = {}
 
 --- Auto-open target file when a coder file is opened directly
 function M.auto_open_target_file()
-	local window = require("codetyper.window")
+	local window = require("codetyper.adapters.nvim.windows")
 
 	-- Skip if split is already open
 	if window.is_open() then
@@ -1508,7 +1508,7 @@ function M.open_coder_companion(open_split)
 
 	if open_split then
 		-- Use the window module to open split view
-		local window = require("codetyper.window")
+		local window = require("codetyper.adapters.nvim.windows")
 		window.open_split(coder_path, filepath)
 	else
 		-- Just open the coder file
diff --git a/lua/codetyper/cmp_source/init.lua b/lua/codetyper/adapters/nvim/cmp/init.lua
similarity index 100%
rename from lua/codetyper/cmp_source/init.lua
rename to lua/codetyper/adapters/nvim/cmp/init.lua
diff --git a/lua/codetyper/commands.lua b/lua/codetyper/adapters/nvim/commands.lua
similarity index 92%
rename from lua/codetyper/commands.lua
rename to lua/codetyper/adapters/nvim/commands.lua
index eb27810..d1f0878 100644
--- a/lua/codetyper/commands.lua
+++ b/lua/codetyper/adapters/nvim/commands.lua
@@ -2,8 +2,8 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
-local window = require("codetyper.window")
+local utils = require("codetyper.support.utils")
+local window = require("codetyper.adapters.nvim.windows")
 
 --- Open coder view for current file or select one
 ---@param opts? table Command options
@@ -108,7 +108,7 @@ end
 --- Process prompt at cursor and generate code
 local function cmd_process()
   local parser = require("codetyper.parser")
-  local llm = require("codetyper.llm")
+  local llm = require("codetyper.core.llm")
 
   local bufnr = vim.api.nvim_get_current_buf()
   local current_file = vim.fn.expand("%:p")
@@ -153,7 +153,7 @@ end
 local function cmd_status()
   local codetyper = require("codetyper")
   local config = codetyper.get_config()
-  local tree = require("codetyper.tree")
+  local tree = require("codetyper.support.tree")
 
   local stats = tree.get_stats()
 
@@ -195,7 +195,7 @@ end
 
 --- Refresh tree.log manually
 local function cmd_tree()
-  local tree = require("codetyper.tree")
+  local tree = require("codetyper.support.tree")
   if tree.update_tree_log() then
     utils.notify("Tree log updated: " .. tree.get_tree_log_path())
   else
@@ -205,7 +205,7 @@ end
 
 --- Open tree.log file
 local function cmd_tree_view()
-  local tree = require("codetyper.tree")
+  local tree = require("codetyper.support.tree")
   local tree_log_path = tree.get_tree_log_path()
 
   if not tree_log_path then
@@ -224,63 +224,63 @@ end
 
 --- Reset processed prompts to allow re-processing
 local function cmd_reset()
-  local autocmds = require("codetyper.autocmds")
+  local autocmds = require("codetyper.adapters.nvim.autocmds")
   autocmds.reset_processed()
 end
 
 --- Force update gitignore
 local function cmd_gitignore()
-  local gitignore = require("codetyper.gitignore")
+  local gitignore = require("codetyper.support.gitignore")
   gitignore.force_update()
 end
 
 --- Open ask panel (with optional visual selection)
 ---@param selection table|nil Visual selection info
 local function cmd_ask(selection)
-  local ask = require("codetyper.ask")
+  local ask = require("codetyper.features.ask.engine")
   ask.open(selection)
 end
 
 --- Close ask panel
 local function cmd_ask_close()
-  local ask = require("codetyper.ask")
+  local ask = require("codetyper.features.ask.engine")
   ask.close()
 end
 
 --- Toggle ask panel
 local function cmd_ask_toggle()
-  local ask = require("codetyper.ask")
+  local ask = require("codetyper.features.ask.engine")
   ask.toggle()
 end
 
 --- Clear ask history
 local function cmd_ask_clear()
-  local ask = require("codetyper.ask")
+  local ask = require("codetyper.features.ask.engine")
   ask.clear_history()
 end
 
 --- Open agent panel (with optional visual selection)
 ---@param selection table|nil Visual selection info
 local function cmd_agent(selection)
-  local agent_ui = require("codetyper.agent.ui")
+  local agent_ui = require("codetyper.adapters.nvim.ui.chat")
   agent_ui.open(selection)
 end
 
 --- Close agent panel
 local function cmd_agent_close()
-  local agent_ui = require("codetyper.agent.ui")
+  local agent_ui = require("codetyper.adapters.nvim.ui.chat")
   agent_ui.close()
 end
 
 --- Toggle agent panel
 local function cmd_agent_toggle()
-  local agent_ui = require("codetyper.agent.ui")
+  local agent_ui = require("codetyper.adapters.nvim.ui.chat")
   agent_ui.toggle()
 end
 
 --- Stop running agent
 local function cmd_agent_stop()
-  local agent = require("codetyper.agent")
+  local agent = require("codetyper.features.agents")
   if agent.is_running() then
     agent.stop()
     utils.notify("Agent stopped")
@@ -293,9 +293,9 @@ end
 ---@param task string The task to accomplish
 ---@param agent_name? string Optional agent name
 local function cmd_agentic_run(task, agent_name)
-  local agentic = require("codetyper.agent.agentic")
-  local logs_panel = require("codetyper.logs_panel")
-  local logs = require("codetyper.agent.logs")
+  local agentic = require("codetyper.features.agents.engine")
+  local logs_panel = require("codetyper.adapters.nvim.ui.logs_panel")
+  local logs = require("codetyper.adapters.nvim.ui.logs")
 
   -- Open logs panel
   logs_panel.open()
@@ -355,7 +355,7 @@ end
 
 --- List available agents
 local function cmd_agentic_list()
-  local agentic = require("codetyper.agent.agentic")
+  local agentic = require("codetyper.features.agents.engine")
   local agents = agentic.list_agents()
 
   local lines = {
@@ -379,7 +379,7 @@ end
 
 --- Initialize .coder/agents/ and .coder/rules/ directories
 local function cmd_agentic_init()
-  local agentic = require("codetyper.agent.agentic")
+  local agentic = require("codetyper.features.agents.engine")
   agentic.init()
 
   local agents_dir = vim.fn.getcwd() .. "/.coder/agents"
@@ -409,14 +409,14 @@ end
 
 --- Toggle logs panel
 local function cmd_logs_toggle()
-  local logs_panel = require("codetyper.logs_panel")
+  local logs_panel = require("codetyper.adapters.nvim.ui.logs_panel")
   logs_panel.toggle()
 end
 
 --- Show scheduler status and queue info
 local function cmd_queue_status()
-  local scheduler = require("codetyper.agent.scheduler")
-  local queue = require("codetyper.agent.queue")
+  local scheduler = require("codetyper.core.scheduler.scheduler")
+  local queue = require("codetyper.core.events.queue")
   local parser = require("codetyper.parser")
 
   local status = scheduler.status()
@@ -455,8 +455,8 @@ end
 
 --- Manually trigger queue processing for current buffer
 local function cmd_queue_process()
-  local autocmds = require("codetyper.autocmds")
-  local logs_panel = require("codetyper.logs_panel")
+  local autocmds = require("codetyper.adapters.nvim.autocmds")
+  local logs_panel = require("codetyper.adapters.nvim.ui.logs_panel")
 
   -- Open logs panel to show progress
   logs_panel.open()
@@ -487,9 +487,9 @@ end
 --- Uses the same processing logic as automatic mode for consistent results
 local function cmd_transform()
   local parser = require("codetyper.parser")
-  local autocmds = require("codetyper.autocmds")
-  local logs_panel = require("codetyper.logs_panel")
-  local logs = require("codetyper.agent.logs")
+  local autocmds = require("codetyper.adapters.nvim.autocmds")
+  local logs_panel = require("codetyper.adapters.nvim.ui.logs_panel")
+  local logs = require("codetyper.adapters.nvim.ui.logs")
 
   local bufnr = vim.api.nvim_get_current_buf()
   local filepath = vim.fn.expand("%:p")
@@ -527,9 +527,9 @@ end
 ---@param end_line number End line (1-indexed)
 local function cmd_transform_range(start_line, end_line)
   local parser = require("codetyper.parser")
-  local autocmds = require("codetyper.autocmds")
-  local logs_panel = require("codetyper.logs_panel")
-  local logs = require("codetyper.agent.logs")
+  local autocmds = require("codetyper.adapters.nvim.autocmds")
+  local logs_panel = require("codetyper.adapters.nvim.ui.logs_panel")
+  local logs = require("codetyper.adapters.nvim.ui.logs")
 
   local bufnr = vim.api.nvim_get_current_buf()
   local filepath = vim.fn.expand("%:p")
@@ -579,7 +579,7 @@ end
 
 --- Index the entire project
 local function cmd_index_project()
-  local indexer = require("codetyper.indexer")
+  local indexer = require("codetyper.features.indexer")
 
   utils.notify("Indexing project...", vim.log.levels.INFO)
 
@@ -601,8 +601,8 @@ end
 
 --- Show index status
 local function cmd_index_status()
-  local indexer = require("codetyper.indexer")
-  local memory = require("codetyper.indexer.memory")
+  local indexer = require("codetyper.features.indexer")
+  local memory = require("codetyper.features.indexer.memory")
 
   local status = indexer.get_status()
   local mem_stats = memory.get_stats()
@@ -639,7 +639,7 @@ end
 
 --- Show learned memories
 local function cmd_memories()
-  local memory = require("codetyper.indexer.memory")
+  local memory = require("codetyper.features.indexer.memory")
 
   local all = memory.get_all()
   local lines = {
@@ -684,7 +684,7 @@ end
 --- Clear memories
 ---@param pattern string|nil Optional pattern to match
 local function cmd_forget(pattern)
-  local memory = require("codetyper.indexer.memory")
+  local memory = require("codetyper.features.indexer.memory")
 
   if not pattern or pattern == "" then
     -- Confirm before clearing all
@@ -706,9 +706,9 @@ end
 --- Uses the same processing logic as automatic mode for consistent results
 local function cmd_transform_at_cursor()
   local parser = require("codetyper.parser")
-  local autocmds = require("codetyper.autocmds")
-  local logs_panel = require("codetyper.logs_panel")
-  local logs = require("codetyper.agent.logs")
+  local autocmds = require("codetyper.adapters.nvim.autocmds")
+  local logs_panel = require("codetyper.adapters.nvim.ui.logs_panel")
+  local logs = require("codetyper.adapters.nvim.ui.logs")
 
   local bufnr = vim.api.nvim_get_current_buf()
   local filepath = vim.fn.expand("%:p")
@@ -741,7 +741,7 @@ end
 ---@param args table Command arguments
 --- Show LLM accuracy statistics
 local function cmd_llm_stats()
-  local llm = require("codetyper.llm")
+  local llm = require("codetyper.core.llm")
   local stats = llm.get_accuracy_stats()
 
   local lines = {
@@ -769,13 +769,13 @@ end
 --- Report feedback on last LLM response
 ---@param was_good boolean Whether the response was good
 local function cmd_llm_feedback(was_good)
-  local llm = require("codetyper.llm")
+  local llm = require("codetyper.core.llm")
   -- Get the last used provider from logs or default
   local provider = "ollama" -- Default assumption
 
   -- Try to get actual last provider from logs
   pcall(function()
-    local logs = require("codetyper.agent.logs")
+    local logs = require("codetyper.adapters.nvim.ui.logs")
     local entries = logs.get(10)
     for i = #entries, 1, -1 do
       local entry = entries[i]
@@ -793,7 +793,7 @@ end
 
 --- Reset LLM accuracy statistics
 local function cmd_llm_reset_stats()
-  local selector = require("codetyper.llm.selector")
+  local selector = require("codetyper.core.llm.selector")
   selector.reset_accuracy_stats()
   utils.notify("LLM accuracy statistics reset", vim.log.levels.INFO)
 end
@@ -877,11 +877,11 @@ local function coder_cmd(args)
     ["llm-reset-stats"] = cmd_llm_reset_stats,
     -- Cost tracking commands
     ["cost"] = function()
-      local cost = require("codetyper.cost")
+      local cost = require("codetyper.core.cost")
       cost.toggle()
     end,
     ["cost-clear"] = function()
-      local cost = require("codetyper.cost")
+      local cost = require("codetyper.core.cost")
       cost.clear()
     end,
     -- Credentials management commands
@@ -1069,7 +1069,7 @@ function M.setup()
 
   -- Index command - open coder companion for current file
   vim.api.nvim_create_user_command("CoderIndex", function()
-    local autocmds = require("codetyper.autocmds")
+    local autocmds = require("codetyper.adapters.nvim.autocmds")
     autocmds.open_coder_companion()
   end, { desc = "Open coder companion for current file" })
 
@@ -1137,7 +1137,7 @@ function M.setup()
 
   -- Brain feedback command - teach the brain from your experience
   vim.api.nvim_create_user_command("CoderFeedback", function(opts)
-    local brain = require("codetyper.brain")
+    local brain = require("codetyper.core.memory")
     if not brain.is_initialized() then
       vim.notify("Brain not initialized", vim.log.levels.WARN)
       return
@@ -1197,7 +1197,7 @@ function M.setup()
 
   -- Brain stats command
   vim.api.nvim_create_user_command("CoderBrain", function(opts)
-    local brain = require("codetyper.brain")
+    local brain = require("codetyper.core.memory")
     if not brain.is_initialized() then
       vim.notify("Brain not initialized", vim.log.levels.WARN)
       return
@@ -1251,7 +1251,7 @@ function M.setup()
 
   -- Cost estimation command
   vim.api.nvim_create_user_command("CoderCost", function()
-    local cost = require("codetyper.cost")
+    local cost = require("codetyper.core.cost")
     cost.toggle()
   end, { desc = "Show LLM cost estimation window" })
 
@@ -1315,14 +1315,14 @@ function M.setup()
 
   -- Conflict mode commands
   vim.api.nvim_create_user_command("CoderConflictToggle", function()
-    local patch = require("codetyper.agent.patch")
+    local patch = require("codetyper.core.diff.patch")
     local current = patch.is_conflict_mode()
     patch.configure({ use_conflict_mode = not current })
     utils.notify("Conflict mode " .. (not current and "enabled" or "disabled"), vim.log.levels.INFO)
   end, { desc = "Toggle conflict mode for code changes" })
 
   vim.api.nvim_create_user_command("CoderConflictResolveAll", function(opts)
-    local conflict = require("codetyper.agent.conflict")
+    local conflict = require("codetyper.core.diff.conflict")
     local bufnr = vim.api.nvim_get_current_buf()
     local keep = opts.args ~= "" and opts.args or "theirs"
     if not vim.tbl_contains({ "ours", "theirs", "both", "none" }, keep) then
@@ -1338,18 +1338,18 @@ function M.setup()
   })
 
   vim.api.nvim_create_user_command("CoderConflictNext", function()
-    local conflict = require("codetyper.agent.conflict")
+    local conflict = require("codetyper.core.diff.conflict")
     conflict.goto_next(vim.api.nvim_get_current_buf())
   end, { desc = "Go to next conflict" })
 
   vim.api.nvim_create_user_command("CoderConflictPrev", function()
-    local conflict = require("codetyper.agent.conflict")
+    local conflict = require("codetyper.core.diff.conflict")
     conflict.goto_prev(vim.api.nvim_get_current_buf())
   end, { desc = "Go to previous conflict" })
 
   vim.api.nvim_create_user_command("CoderConflictStatus", function()
-    local conflict = require("codetyper.agent.conflict")
-    local patch = require("codetyper.agent.patch")
+    local conflict = require("codetyper.core.diff.conflict")
+    local patch = require("codetyper.core.diff.patch")
     local bufnr = vim.api.nvim_get_current_buf()
     local count = conflict.count_conflicts(bufnr)
     local mode = patch.is_conflict_mode() and "enabled" or "disabled"
@@ -1357,7 +1357,7 @@ function M.setup()
   end, { desc = "Show conflict status" })
 
   vim.api.nvim_create_user_command("CoderConflictMenu", function()
-    local conflict = require("codetyper.agent.conflict")
+    local conflict = require("codetyper.core.diff.conflict")
     local bufnr = vim.api.nvim_get_current_buf()
     -- Ensure conflicts are processed first (sets up highlights and keymaps)
     conflict.process(bufnr)
@@ -1366,35 +1366,35 @@ function M.setup()
 
   -- Manual commands to accept conflicts
   vim.api.nvim_create_user_command("CoderConflictAcceptCurrent", function()
-    local conflict = require("codetyper.agent.conflict")
+    local conflict = require("codetyper.core.diff.conflict")
     local bufnr = vim.api.nvim_get_current_buf()
     conflict.process(bufnr) -- Ensure keymaps are set up
     conflict.accept_ours(bufnr)
   end, { desc = "Accept current (original) code" })
 
   vim.api.nvim_create_user_command("CoderConflictAcceptIncoming", function()
-    local conflict = require("codetyper.agent.conflict")
+    local conflict = require("codetyper.core.diff.conflict")
     local bufnr = vim.api.nvim_get_current_buf()
     conflict.process(bufnr) -- Ensure keymaps are set up
     conflict.accept_theirs(bufnr)
   end, { desc = "Accept incoming (AI) code" })
 
   vim.api.nvim_create_user_command("CoderConflictAcceptBoth", function()
-    local conflict = require("codetyper.agent.conflict")
+    local conflict = require("codetyper.core.diff.conflict")
     local bufnr = vim.api.nvim_get_current_buf()
     conflict.process(bufnr)
     conflict.accept_both(bufnr)
   end, { desc = "Accept both versions" })
 
   vim.api.nvim_create_user_command("CoderConflictAcceptNone", function()
-    local conflict = require("codetyper.agent.conflict")
+    local conflict = require("codetyper.core.diff.conflict")
     local bufnr = vim.api.nvim_get_current_buf()
     conflict.process(bufnr)
     conflict.accept_none(bufnr)
   end, { desc = "Delete conflict (accept none)" })
 
   vim.api.nvim_create_user_command("CoderConflictAutoMenu", function()
-    local conflict = require("codetyper.agent.conflict")
+    local conflict = require("codetyper.core.diff.conflict")
     local conf = conflict.get_config()
     local new_state = not conf.auto_show_menu
     conflict.configure({ auto_show_menu = new_state, auto_show_next_menu = new_state })
@@ -1402,12 +1402,12 @@ function M.setup()
   end, { desc = "Toggle auto-show conflict menu after code injection" })
 
   -- Initialize conflict module
-  local conflict = require("codetyper.agent.conflict")
+  local conflict = require("codetyper.core.diff.conflict")
   conflict.setup()
 
   -- Linter validation commands
   vim.api.nvim_create_user_command("CoderLintCheck", function()
-    local linter = require("codetyper.agent.linter")
+    local linter = require("codetyper.features.agents.linter")
     local bufnr = vim.api.nvim_get_current_buf()
     linter.validate_after_injection(bufnr, nil, nil, function(result)
       if result then
@@ -1419,7 +1419,7 @@ function M.setup()
   end, { desc = "Check current buffer for lint errors" })
 
   vim.api.nvim_create_user_command("CoderLintFix", function()
-    local linter = require("codetyper.agent.linter")
+    local linter = require("codetyper.features.agents.linter")
     local bufnr = vim.api.nvim_get_current_buf()
     local line_count = vim.api.nvim_buf_line_count(bufnr)
     local result = linter.check_region(bufnr, 1, line_count)
@@ -1431,7 +1431,7 @@ function M.setup()
   end, { desc = "Request AI to fix lint errors in current buffer" })
 
   vim.api.nvim_create_user_command("CoderLintQuickfix", function()
-    local linter = require("codetyper.agent.linter")
+    local linter = require("codetyper.features.agents.linter")
     local bufnr = vim.api.nvim_get_current_buf()
     local line_count = vim.api.nvim_buf_line_count(bufnr)
     local result = linter.check_region(bufnr, 1, line_count)
@@ -1443,8 +1443,8 @@ function M.setup()
   end, { desc = "Show lint errors in quickfix list" })
 
   vim.api.nvim_create_user_command("CoderLintToggleAuto", function()
-    local conflict = require("codetyper.agent.conflict")
-    local linter = require("codetyper.agent.linter")
+    local conflict = require("codetyper.core.diff.conflict")
+    local linter = require("codetyper.features.agents.linter")
     local linter_config = linter.get_config()
     local new_state = not linter_config.auto_save
     linter.configure({ auto_save = new_state })
diff --git a/lua/codetyper/agent/ui.lua b/lua/codetyper/adapters/nvim/ui/chat.lua
similarity index 99%
rename from lua/codetyper/agent/ui.lua
rename to lua/codetyper/adapters/nvim/ui/chat.lua
index 6ae9709..0b697c3 100644
--- a/lua/codetyper/agent/ui.lua
+++ b/lua/codetyper/adapters/nvim/ui/chat.lua
@@ -4,9 +4,9 @@
 
 local M = {}
 
-local agent = require("codetyper.agent")
-local logs = require("codetyper.agent.logs")
-local utils = require("codetyper.utils")
+local agent = require("codetyper.features.agents")
+local logs = require("codetyper.adapters.nvim.ui.logs")
+local utils = require("codetyper.support.utils")
 
 ---@class AgentUIState
 ---@field chat_buf number|nil Chat buffer
@@ -321,7 +321,7 @@ local function submit_input()
       vim.bo[state.chat_buf].modifiable = false
     end
     -- Also clear collected diffs
-    local diff_review = require("codetyper.agent.diff_review")
+    local diff_review = require("codetyper.adapters.nvim.ui.diff_review")
     diff_review.clear()
     return
   end
@@ -387,7 +387,7 @@ local function submit_input()
     current_file = vim.fn.expand("%:p")
   end
 
-  local llm = require("codetyper.llm")
+  local llm = require("codetyper.core.llm")
   local context = {}
 
   if current_file ~= "" and vim.fn.filereadable(current_file) == 1 then
diff --git a/lua/codetyper/agent/context_modal.lua b/lua/codetyper/adapters/nvim/ui/context_modal.lua
similarity index 99%
rename from lua/codetyper/agent/context_modal.lua
rename to lua/codetyper/adapters/nvim/ui/context_modal.lua
index ea515e1..be772e7 100644
--- a/lua/codetyper/agent/context_modal.lua
+++ b/lua/codetyper/adapters/nvim/ui/context_modal.lua
@@ -304,7 +304,7 @@ function M.open(original_event, llm_response, callback, suggested_commands)
 
 	-- Log
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "info",
 			message = "Context modal opened - waiting for user input",
diff --git a/lua/codetyper/agent/diff_review.lua b/lua/codetyper/adapters/nvim/ui/diff_review.lua
similarity index 99%
rename from lua/codetyper/agent/diff_review.lua
rename to lua/codetyper/adapters/nvim/ui/diff_review.lua
index cbe8cf0..ff71c0f 100644
--- a/lua/codetyper/agent/diff_review.lua
+++ b/lua/codetyper/adapters/nvim/ui/diff_review.lua
@@ -5,7 +5,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 local prompts = require("codetyper.prompts.agent.diff")
 
 
diff --git a/lua/codetyper/agent/logs.lua b/lua/codetyper/adapters/nvim/ui/logs.lua
similarity index 100%
rename from lua/codetyper/agent/logs.lua
rename to lua/codetyper/adapters/nvim/ui/logs.lua
diff --git a/lua/codetyper/logs_panel.lua b/lua/codetyper/adapters/nvim/ui/logs_panel.lua
similarity index 99%
rename from lua/codetyper/logs_panel.lua
rename to lua/codetyper/adapters/nvim/ui/logs_panel.lua
index 789b127..25cdfb4 100644
--- a/lua/codetyper/logs_panel.lua
+++ b/lua/codetyper/adapters/nvim/ui/logs_panel.lua
@@ -4,8 +4,8 @@
 
 local M = {}
 
-local logs = require("codetyper.agent.logs")
-local queue = require("codetyper.agent.queue")
+local logs = require("codetyper.adapters.nvim.ui.logs")
+local queue = require("codetyper.core.events.queue")
 
 ---@class LogsPanelState
 ---@field buf number|nil Logs buffer
diff --git a/lua/codetyper/chat_switcher.lua b/lua/codetyper/adapters/nvim/ui/switcher.lua
similarity index 88%
rename from lua/codetyper/chat_switcher.lua
rename to lua/codetyper/adapters/nvim/ui/switcher.lua
index 09f9bef..c65ad05 100644
--- a/lua/codetyper/chat_switcher.lua
+++ b/lua/codetyper/adapters/nvim/ui/switcher.lua
@@ -20,8 +20,8 @@ function M.show()
     end
 
     -- Close current panel first
-    local ask = require("codetyper.ask")
-    local agent_ui = require("codetyper.agent.ui")
+    local ask = require("codetyper.features.ask.engine")
+    local agent_ui = require("codetyper.adapters.nvim.ui.chat")
 
     if ask.is_open() then
       ask.close()
diff --git a/lua/codetyper/window.lua b/lua/codetyper/adapters/nvim/windows.lua
similarity index 97%
rename from lua/codetyper/window.lua
rename to lua/codetyper/adapters/nvim/windows.lua
index 27d2ce4..31b04dc 100644
--- a/lua/codetyper/window.lua
+++ b/lua/codetyper/adapters/nvim/windows.lua
@@ -2,7 +2,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 ---@type number|nil Current coder window ID
 M._coder_win = nil
@@ -43,7 +43,7 @@ function M.open_split(target_path, coder_path)
     utils.write_file(coder_path, "")
     
     -- Ensure gitignore is updated when creating a new coder file
-    local gitignore = require("codetyper.gitignore")
+    local gitignore = require("codetyper.support.gitignore")
     gitignore.ensure_ignored()
   end
 
diff --git a/lua/codetyper/credentials.lua b/lua/codetyper/config/credentials.lua
similarity index 99%
rename from lua/codetyper/credentials.lua
rename to lua/codetyper/config/credentials.lua
index 18f9880..837b9e4 100644
--- a/lua/codetyper/credentials.lua
+++ b/lua/codetyper/config/credentials.lua
@@ -6,7 +6,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Get the credentials file path
 ---@return string Path to credentials file
diff --git a/lua/codetyper/config.lua b/lua/codetyper/config/defaults.lua
similarity index 100%
rename from lua/codetyper/config.lua
rename to lua/codetyper/config/defaults.lua
diff --git a/lua/codetyper/preferences.lua b/lua/codetyper/config/preferences.lua
similarity index 99%
rename from lua/codetyper/preferences.lua
rename to lua/codetyper/config/preferences.lua
index ec28f4f..0c3c0da 100644
--- a/lua/codetyper/preferences.lua
+++ b/lua/codetyper/config/preferences.lua
@@ -6,7 +6,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 ---@class CoderPreferences
 ---@field auto_process boolean Whether to auto-process /@ @/ tags (default: nil = ask)
diff --git a/lua/codetyper/cost.lua b/lua/codetyper/core/cost/init.lua
similarity index 99%
rename from lua/codetyper/cost.lua
rename to lua/codetyper/core/cost/init.lua
index 33c3442..e304998 100644
--- a/lua/codetyper/cost.lua
+++ b/lua/codetyper/core/cost/init.lua
@@ -6,7 +6,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Cost history file name
 local COST_HISTORY_FILE = "cost_history.json"
diff --git a/lua/codetyper/agent/conflict.lua b/lua/codetyper/core/diff/conflict.lua
similarity index 99%
rename from lua/codetyper/agent/conflict.lua
rename to lua/codetyper/core/diff/conflict.lua
index 141b593..f5bfb52 100644
--- a/lua/codetyper/agent/conflict.lua
+++ b/lua/codetyper/core/diff/conflict.lua
@@ -19,7 +19,7 @@ local params = require("codetyper.params.agent.conflict")
 
 --- Lazy load linter module
 local function get_linter()
-	return require("codetyper.agent.linter")
+	return require("codetyper.features.agents.linter")
 end
 
 --- Configuration
@@ -66,7 +66,7 @@ local function validate_after_accept(bufnr, start_line, end_line, accepted_type)
 		-- If errors found and auto-fix is enabled, queue fix automatically
 		if result.has_errors and config.auto_fix_lint_errors then
 			pcall(function()
-				local logs = require("codetyper.agent.logs")
+				local logs = require("codetyper.adapters.nvim.ui.logs")
 				logs.add({
 					type = "info",
 					message = "Auto-queuing fix for lint errors...",
@@ -954,7 +954,7 @@ function M.process(bufnr)
 
 		-- Log
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.info(string.format("Found %d conflict(s) - use co/ct/cb/cn to resolve, [x/]x to navigate", #conflicts))
 		end)
 	else
diff --git a/lua/codetyper/agent/diff.lua b/lua/codetyper/core/diff/diff.lua
similarity index 99%
rename from lua/codetyper/agent/diff.lua
rename to lua/codetyper/core/diff/diff.lua
index 1dde651..2870436 100644
--- a/lua/codetyper/agent/diff.lua
+++ b/lua/codetyper/core/diff/diff.lua
@@ -178,7 +178,7 @@ end
 ---@param command string The bash command to approve
 ---@param callback fun(result: BashApprovalResult) Called with user decision
 function M.show_bash_approval(command, callback)
-  local permissions = require("codetyper.agent.permissions")
+  local permissions = require("codetyper.features.agents.permissions")
 
   -- Check if command is auto-approved
   local perm_result = permissions.check_bash_permission(command)
diff --git a/lua/codetyper/agent/patch.lua b/lua/codetyper/core/diff/patch.lua
similarity index 96%
rename from lua/codetyper/agent/patch.lua
rename to lua/codetyper/core/diff/patch.lua
index fdb5d43..97916e7 100644
--- a/lua/codetyper/agent/patch.lua
+++ b/lua/codetyper/core/diff/patch.lua
@@ -12,17 +12,17 @@ local params = require("codetyper.params.agent.patch")
 
 --- Lazy load inject module to avoid circular requires
 local function get_inject_module()
-	return require("codetyper.agent.inject")
+	return require("codetyper.inject")
 end
 
 --- Lazy load search_replace module
 local function get_search_replace_module()
-	return require("codetyper.agent.search_replace")
+	return require("codetyper.core.diff.search_replace")
 end
 
 --- Lazy load conflict module
 local function get_conflict_module()
-	return require("codetyper.agent.conflict")
+	return require("codetyper.core.diff.conflict")
 end
 
 --- Configuration for patch behavior
@@ -170,7 +170,7 @@ function M.queue_patch(patch)
 
 	-- Log patch creation
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "patch",
 			message = string.format(
@@ -236,14 +236,14 @@ function M.create_from_event(event, generated_code, confidence, strategy)
 	if use_search_replace then
 		injection_strategy = "search_replace"
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.add({
 				type = "info",
 				message = string.format("Using SEARCH/REPLACE mode with %d block(s)", #sr_blocks),
 			})
 		end)
 	elseif not injection_strategy and event.intent then
-		local intent_mod = require("codetyper.agent.intent")
+		local intent_mod = require("codetyper.core.intent")
 		if intent_mod.is_replacement(event.intent) then
 			injection_strategy = "replace"
 
@@ -255,7 +255,7 @@ function M.create_from_event(event, generated_code, confidence, strategy)
 					end_line = event.range.end_line,
 				}
 				pcall(function()
-					local logs = require("codetyper.agent.logs")
+					local logs = require("codetyper.adapters.nvim.ui.logs")
 					logs.add({
 						type = "info",
 						message = string.format("Inline prompt: will replace tag region (lines %d-%d)",
@@ -273,7 +273,7 @@ function M.create_from_event(event, generated_code, confidence, strategy)
 					end_line = event.range.end_line,
 				}
 				pcall(function()
-					local logs = require("codetyper.agent.logs")
+					local logs = require("codetyper.adapters.nvim.ui.logs")
 					logs.add({
 						type = "warning",
 						message = "No scope found, using tag range as fallback",
@@ -510,7 +510,7 @@ function M.apply(patch)
 		M.mark_stale(patch.id, stale_reason)
 
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.add({
 				type = "warning",
 				message = string.format("Patch %s is stale: %s", patch.id, stale_reason or "unknown"),
@@ -549,7 +549,7 @@ function M.apply(patch)
 
 		pcall(function()
 			if tags_removed > 0 then
-				local logs = require("codetyper.agent.logs")
+				local logs = require("codetyper.adapters.nvim.ui.logs")
 				local source_name = vim.api.nvim_buf_get_name(source_bufnr)
 				logs.add({
 					type = "info",
@@ -573,7 +573,7 @@ function M.apply(patch)
 			tags_removed = remove_prompt_tags(source_bufnr)
 			if tags_removed > 0 then
 				pcall(function()
-					local logs = require("codetyper.agent.logs")
+					local logs = require("codetyper.adapters.nvim.ui.logs")
 					logs.add({
 						type = "info",
 						message = string.format("Removed %d prompt tag(s)", tags_removed),
@@ -589,7 +589,7 @@ function M.apply(patch)
 			M.mark_applied(patch.id)
 
 			pcall(function()
-				local logs = require("codetyper.agent.logs")
+				local logs = require("codetyper.adapters.nvim.ui.logs")
 				logs.add({
 					type = "success",
 					message = string.format("Patch %s applied via SEARCH/REPLACE (%d block(s))",
@@ -603,7 +603,7 @@ function M.apply(patch)
 
 			-- Learn from successful code generation
 			pcall(function()
-				local brain = require("codetyper.brain")
+				local brain = require("codetyper.core.memory")
 				if brain.is_initialized() then
 					local intent_type = patch.intent and patch.intent.type or "unknown"
 					brain.learn({
@@ -624,7 +624,7 @@ function M.apply(patch)
 		else
 			-- SEARCH/REPLACE failed, log the error
 			pcall(function()
-				local logs = require("codetyper.agent.logs")
+				local logs = require("codetyper.adapters.nvim.ui.logs")
 				logs.add({
 					type = "warning",
 					message = string.format("SEARCH/REPLACE failed: %s. Falling back to line-based injection.", err or "unknown"),
@@ -723,7 +723,7 @@ function M.apply(patch)
 		-- Log inline prompt handling
 		if is_inline_prompt then
 			pcall(function()
-				local logs = require("codetyper.agent.logs")
+				local logs = require("codetyper.adapters.nvim.ui.logs")
 				logs.add({
 					type = "info",
 					message = string.format("Inline prompt: replacing lines %d-%d",
@@ -738,7 +738,7 @@ function M.apply(patch)
 
 		-- Log injection details
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			if inject_result.imports_added > 0 then
 				logs.add({
 					type = "info",
@@ -766,7 +766,7 @@ function M.apply(patch)
 	M.mark_applied(patch.id)
 
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "success",
 			message = string.format("Patch %s applied successfully", patch.id),
@@ -780,7 +780,7 @@ function M.apply(patch)
 	-- Learn from successful code generation - this builds neural pathways
 	-- The more code is successfully applied, the better the brain becomes
 	pcall(function()
-		local brain = require("codetyper.brain")
+		local brain = require("codetyper.core.memory")
 		if brain.is_initialized() then
 			-- Learn the successful pattern
 			local intent_type = patch.intent and patch.intent.type or "unknown"
@@ -1010,7 +1010,7 @@ function M.apply_with_conflict(patch)
 			M.mark_applied(patch.id)
 
 			pcall(function()
-				local logs = require("codetyper.agent.logs")
+				local logs = require("codetyper.adapters.nvim.ui.logs")
 				logs.add({
 					type = "success",
 					message = string.format(
@@ -1044,7 +1044,7 @@ function M.apply_with_conflict(patch)
 		M.mark_applied(patch.id)
 
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.add({
 				type = "success",
 				message = "Created conflict for review - use co/ct/cb/cn to resolve",
diff --git a/lua/codetyper/agent/search_replace.lua b/lua/codetyper/core/diff/search_replace.lua
similarity index 100%
rename from lua/codetyper/agent/search_replace.lua
rename to lua/codetyper/core/diff/search_replace.lua
diff --git a/lua/codetyper/agent/queue.lua b/lua/codetyper/core/events/queue.lua
similarity index 99%
rename from lua/codetyper/agent/queue.lua
rename to lua/codetyper/core/events/queue.lua
index 9c763c1..002cd3b 100644
--- a/lua/codetyper/agent/queue.lua
+++ b/lua/codetyper/core/events/queue.lua
@@ -194,7 +194,7 @@ function M.enqueue(event)
 
 	-- Log to agent logs if available
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "queue",
 			message = string.format("Event queued: %s (priority: %d)", event.id, event.priority),
diff --git a/lua/codetyper/agent/intent.lua b/lua/codetyper/core/intent/init.lua
similarity index 100%
rename from lua/codetyper/agent/intent.lua
rename to lua/codetyper/core/intent/init.lua
diff --git a/lua/codetyper/agent/confidence.lua b/lua/codetyper/core/llm/confidence.lua
similarity index 98%
rename from lua/codetyper/agent/confidence.lua
rename to lua/codetyper/core/llm/confidence.lua
index 4be2b3b..1ac14c8 100644
--- a/lua/codetyper/agent/confidence.lua
+++ b/lua/codetyper/core/llm/confidence.lua
@@ -74,7 +74,7 @@ local function score_syntax(response)
 	local score = 1.0
 
 	-- Check bracket balance
-	if not require("codetyper.utils").check_brackets(response) then
+	if not require("codetyper.support.utils").check_brackets(response) then
 		score = score - 0.4
 	end
 
diff --git a/lua/codetyper/llm/copilot.lua b/lua/codetyper/core/llm/copilot.lua
similarity index 98%
rename from lua/codetyper/llm/copilot.lua
rename to lua/codetyper/core/llm/copilot.lua
index b7fd44e..17ecc1b 100644
--- a/lua/codetyper/llm/copilot.lua
+++ b/lua/codetyper/core/llm/copilot.lua
@@ -2,8 +2,8 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
-local llm = require("codetyper.llm")
+local utils = require("codetyper.support.utils")
+local llm = require("codetyper.core.llm")
 
 --- Copilot API endpoints
 local AUTH_URL = "https://api.github.com/copilot_internal/v2/token"
@@ -296,7 +296,7 @@ local function make_request(token, body, callback)
 
 			-- Record usage for cost tracking
 			if usage.prompt_tokens or usage.completion_tokens then
-				local cost = require("codetyper.cost")
+				local cost = require("codetyper.core.cost")
 				cost.record_usage(
 					get_model(),
 					usage.prompt_tokens or 0,
@@ -348,7 +348,7 @@ end
 ---@param context table Context information
 ---@param callback fun(response: string|nil, error: string|nil)
 function M.generate(prompt, context, callback)
-	local logs = require("codetyper.agent.logs")
+	local logs = require("codetyper.adapters.nvim.ui.logs")
 
 	ensure_initialized()
 
@@ -414,7 +414,7 @@ end
 ---@param tool_definitions table Tool definitions
 ---@param callback fun(response: table|nil, error: string|nil)
 function M.generate_with_tools(messages, context, tool_definitions, callback)
-	local logs = require("codetyper.agent.logs")
+	local logs = require("codetyper.adapters.nvim.ui.logs")
 
 	ensure_initialized()
 
@@ -436,7 +436,7 @@ function M.generate_with_tools(messages, context, tool_definitions, callback)
 			return
 		end
 
-		local tools_module = require("codetyper.agent.tools")
+		local tools_module = require("codetyper.core.tools")
 		local agent_prompts = require("codetyper.prompts.agent")
 
 		-- Build system prompt with agent instructions and project context
@@ -634,7 +634,7 @@ function M.generate_with_tools(messages, context, tool_definitions, callback)
 					logs.response(response.usage.prompt_tokens or 0, response.usage.completion_tokens or 0, "stop")
 
 					-- Record usage for cost tracking
-					local cost_tracker = require("codetyper.cost")
+					local cost_tracker = require("codetyper.core.cost")
 					cost_tracker.record_usage(
 						get_model(),
 						response.usage.prompt_tokens or 0,
diff --git a/lua/codetyper/llm/gemini.lua b/lua/codetyper/core/llm/gemini.lua
similarity index 97%
rename from lua/codetyper/llm/gemini.lua
rename to lua/codetyper/core/llm/gemini.lua
index d6ebdef..20c081d 100644
--- a/lua/codetyper/llm/gemini.lua
+++ b/lua/codetyper/core/llm/gemini.lua
@@ -2,8 +2,8 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
-local llm = require("codetyper.llm")
+local utils = require("codetyper.support.utils")
+local llm = require("codetyper.core.llm")
 
 --- Gemini API endpoint
 local API_URL = "https://generativelanguage.googleapis.com/v1beta/models"
@@ -167,7 +167,7 @@ end
 ---@param context table Context information
 ---@param callback fun(response: string|nil, error: string|nil) Callback function
 function M.generate(prompt, context, callback)
-	local logs = require("codetyper.agent.logs")
+	local logs = require("codetyper.adapters.nvim.ui.logs")
 	local model = get_model()
 
 	-- Log the request
@@ -217,7 +217,7 @@ end
 ---@param tool_definitions table Tool definitions
 ---@param callback fun(response: table|nil, error: string|nil) Callback with raw response
 function M.generate_with_tools(messages, context, tool_definitions, callback)
-	local logs = require("codetyper.agent.logs")
+	local logs = require("codetyper.adapters.nvim.ui.logs")
 	local model = get_model()
 
 	logs.request("gemini", model)
@@ -230,7 +230,7 @@ function M.generate_with_tools(messages, context, tool_definitions, callback)
 		return
 	end
 
-	local tools_module = require("codetyper.agent.tools")
+	local tools_module = require("codetyper.core.tools")
 	local agent_prompts = require("codetyper.prompts.agent")
 
 	-- Build system prompt with agent instructions
diff --git a/lua/codetyper/llm/init.lua b/lua/codetyper/core/llm/init.lua
similarity index 93%
rename from lua/codetyper/llm/init.lua
rename to lua/codetyper/core/llm/init.lua
index 8e9f003..4a6f5a2 100644
--- a/lua/codetyper/llm/init.lua
+++ b/lua/codetyper/core/llm/init.lua
@@ -1,8 +1,8 @@
 ---@mod codetyper.llm LLM interface for Codetyper.nvim
 
 local M = {}
-local lang_map = require("codetyper.utils.langmap")
-local utils = require("codetyper.utils")
+local lang_map = require("codetyper.support.langmap")
+local utils = require("codetyper.support.utils")
 
 --- Get the appropriate LLM client based on configuration
 ---@return table LLM client module
@@ -11,13 +11,13 @@ function M.get_client()
 	local config = codetyper.get_config()
 
 	if config.llm.provider == "ollama" then
-		return require("codetyper.llm.ollama")
+		return require("codetyper.core.llm.ollama")
 	elseif config.llm.provider == "openai" then
-		return require("codetyper.llm.openai")
+		return require("codetyper.core.llm.openai")
 	elseif config.llm.provider == "gemini" then
-		return require("codetyper.llm.gemini")
+		return require("codetyper.core.llm.gemini")
 	elseif config.llm.provider == "copilot" then
-		return require("codetyper.llm.copilot")
+		return require("codetyper.core.llm.copilot")
 	else
 		error("Unknown LLM provider: " .. config.llm.provider)
 	end
@@ -39,14 +39,14 @@ end
 ---@param context table Context information
 ---@param callback fun(response: string|nil, error: string|nil, metadata: table|nil) Callback
 function M.smart_generate(prompt, context, callback)
-	local selector = require("codetyper.llm.selector")
+	local selector = require("codetyper.core.llm.selector")
 	selector.smart_generate(prompt, context, callback)
 end
 
 --- Get accuracy statistics for providers
 ---@return table Statistics for each provider
 function M.get_accuracy_stats()
-	local selector = require("codetyper.llm.selector")
+	local selector = require("codetyper.core.llm.selector")
 	return selector.get_accuracy_stats()
 end
 
@@ -54,7 +54,7 @@ end
 ---@param provider string Which provider generated the response
 ---@param was_correct boolean Whether the response was good
 function M.report_feedback(provider, was_correct)
-	local selector = require("codetyper.llm.selector")
+	local selector = require("codetyper.core.llm.selector")
 	selector.report_feedback(provider, was_correct)
 end
 
diff --git a/lua/codetyper/llm/ollama.lua b/lua/codetyper/core/llm/ollama.lua
similarity index 97%
rename from lua/codetyper/llm/ollama.lua
rename to lua/codetyper/core/llm/ollama.lua
index 1033c99..aea3fc6 100644
--- a/lua/codetyper/llm/ollama.lua
+++ b/lua/codetyper/core/llm/ollama.lua
@@ -2,8 +2,8 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
-local llm = require("codetyper.llm")
+local utils = require("codetyper.support.utils")
+local llm = require("codetyper.core.llm")
 
 --- Get Ollama host from stored credentials or config
 ---@return string Host URL
@@ -137,7 +137,7 @@ end
 ---@param context table Context information
 ---@param callback fun(response: string|nil, error: string|nil) Callback function
 function M.generate(prompt, context, callback)
-	local logs = require("codetyper.agent.logs")
+	local logs = require("codetyper.adapters.nvim.ui.logs")
 	local model = get_model()
 
 	-- Log the request
@@ -217,9 +217,9 @@ end
 ---@param tool_definitions table Tool definitions
 ---@param callback fun(response: table|nil, error: string|nil) Callback with Claude-like response format
 function M.generate_with_tools(messages, context, tool_definitions, callback)
-	local logs = require("codetyper.agent.logs")
+	local logs = require("codetyper.adapters.nvim.ui.logs")
 	local agent_prompts = require("codetyper.prompts.agent")
-	local tools_module = require("codetyper.agent.tools")
+	local tools_module = require("codetyper.core.tools")
 
 	logs.request("ollama", get_model())
 	logs.thinking("Preparing agent request...")
@@ -322,7 +322,7 @@ function M.generate_with_tools(messages, context, tool_definitions, callback)
 				logs.response(response.prompt_eval_count or 0, response.eval_count or 0, "stop")
 
 				-- Record usage for cost tracking (free for local models)
-				local cost = require("codetyper.cost")
+				local cost = require("codetyper.core.cost")
 				cost.record_usage(
 					get_model(),
 					response.prompt_eval_count or 0,
diff --git a/lua/codetyper/llm/openai.lua b/lua/codetyper/core/llm/openai.lua
similarity index 97%
rename from lua/codetyper/llm/openai.lua
rename to lua/codetyper/core/llm/openai.lua
index 4933945..cb5be26 100644
--- a/lua/codetyper/llm/openai.lua
+++ b/lua/codetyper/core/llm/openai.lua
@@ -2,8 +2,8 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
-local llm = require("codetyper.llm")
+local utils = require("codetyper.support.utils")
+local llm = require("codetyper.core.llm")
 
 --- OpenAI API endpoint
 local API_URL = "https://api.openai.com/v1/chat/completions"
@@ -158,7 +158,7 @@ end
 ---@param context table Context information
 ---@param callback fun(response: string|nil, error: string|nil) Callback function
 function M.generate(prompt, context, callback)
-	local logs = require("codetyper.agent.logs")
+	local logs = require("codetyper.adapters.nvim.ui.logs")
 	local model = get_model()
 
 	-- Log the request
@@ -208,7 +208,7 @@ end
 ---@param tool_definitions table Tool definitions
 ---@param callback fun(response: table|nil, error: string|nil) Callback with raw response
 function M.generate_with_tools(messages, context, tool_definitions, callback)
-	local logs = require("codetyper.agent.logs")
+	local logs = require("codetyper.adapters.nvim.ui.logs")
 	local model = get_model()
 
 	logs.request("openai", model)
@@ -221,7 +221,7 @@ function M.generate_with_tools(messages, context, tool_definitions, callback)
 		return
 	end
 
-	local tools_module = require("codetyper.agent.tools")
+	local tools_module = require("codetyper.core.tools")
 	local agent_prompts = require("codetyper.prompts.agent")
 
 	-- Build system prompt with agent instructions
@@ -310,7 +310,7 @@ function M.generate_with_tools(messages, context, tool_definitions, callback)
 				logs.response(response.usage.prompt_tokens or 0, response.usage.completion_tokens or 0, "stop")
 
 				-- Record usage for cost tracking
-				local cost = require("codetyper.cost")
+				local cost = require("codetyper.core.cost")
 				cost.record_usage(
 					model,
 					response.usage.prompt_tokens or 0,
diff --git a/lua/codetyper/agent/parser.lua b/lua/codetyper/core/llm/parser.lua
similarity index 100%
rename from lua/codetyper/agent/parser.lua
rename to lua/codetyper/core/llm/parser.lua
diff --git a/lua/codetyper/llm/selector.lua b/lua/codetyper/core/llm/selector.lua
similarity index 98%
rename from lua/codetyper/llm/selector.lua
rename to lua/codetyper/core/llm/selector.lua
index aebc21c..429b146 100644
--- a/lua/codetyper/llm/selector.lua
+++ b/lua/codetyper/core/llm/selector.lua
@@ -296,7 +296,7 @@ end
 ---@param callback fun(result: PonderResult) Callback with pondering result
 function M.ponder(prompt, context, ollama_response, callback)
 	-- Use Copilot as verifier
-	local copilot = require("codetyper.llm.copilot")
+	local copilot = require("codetyper.core.llm.copilot")
 
 	-- Build verification prompt
 	local verify_prompt = prompt
@@ -393,7 +393,7 @@ function M.smart_generate(prompt, context, callback)
 
 	-- Log selection
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "info",
 			message = string.format(
@@ -408,9 +408,9 @@ function M.smart_generate(prompt, context, callback)
 	-- Get the selected client
 	local client
 	if selection.provider == "ollama" then
-		client = require("codetyper.llm.ollama")
+		client = require("codetyper.core.llm.ollama")
 	else
-		client = require("codetyper.llm.copilot")
+		client = require("codetyper.core.llm.copilot")
 	end
 
 	-- Generate response
@@ -419,7 +419,7 @@ function M.smart_generate(prompt, context, callback)
 			-- Fallback on error
 			if selection.provider == "ollama" then
 				-- Try Copilot as fallback
-				local copilot = require("codetyper.llm.copilot")
+				local copilot = require("codetyper.core.llm.copilot")
 				copilot.generate(prompt, context, function(fallback_response, fallback_error)
 					callback(fallback_response, fallback_error, {
 						provider = "copilot",
diff --git a/lua/codetyper/brain/delta/commit.lua b/lua/codetyper/core/memory/delta/commit.lua
similarity index 96%
rename from lua/codetyper/brain/delta/commit.lua
rename to lua/codetyper/core/memory/delta/commit.lua
index 9afd60d..d84dad5 100644
--- a/lua/codetyper/brain/delta/commit.lua
+++ b/lua/codetyper/core/memory/delta/commit.lua
@@ -1,10 +1,10 @@
 --- Brain Delta Commit Operations
 --- Git-like commit creation and management
 
-local storage = require("codetyper.brain.storage")
-local hash_mod = require("codetyper.brain.hash")
-local diff_mod = require("codetyper.brain.delta.diff")
-local types = require("codetyper.brain.types")
+local storage = require("codetyper.core.memory.storage")
+local hash_mod = require("codetyper.core.memory.hash")
+local diff_mod = require("codetyper.core.memory.delta.diff")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
diff --git a/lua/codetyper/brain/delta/diff.lua b/lua/codetyper/core/memory/delta/diff.lua
similarity index 99%
rename from lua/codetyper/brain/delta/diff.lua
rename to lua/codetyper/core/memory/delta/diff.lua
index b1d63d6..aeb4213 100644
--- a/lua/codetyper/brain/delta/diff.lua
+++ b/lua/codetyper/core/memory/delta/diff.lua
@@ -1,7 +1,7 @@
 --- Brain Delta Diff Computation
 --- Field-level diff algorithms for delta versioning
 
-local hash = require("codetyper.brain.hash")
+local hash = require("codetyper.core.memory.hash")
 
 local M = {}
 
diff --git a/lua/codetyper/brain/delta/init.lua b/lua/codetyper/core/memory/delta/init.lua
similarity index 87%
rename from lua/codetyper/brain/delta/init.lua
rename to lua/codetyper/core/memory/delta/init.lua
index 7efa8e5..cde1d89 100644
--- a/lua/codetyper/brain/delta/init.lua
+++ b/lua/codetyper/core/memory/delta/init.lua
@@ -1,10 +1,10 @@
 --- Brain Delta Coordinator
 --- Git-like versioning system for brain state
 
-local storage = require("codetyper.brain.storage")
-local commit_mod = require("codetyper.brain.delta.commit")
-local diff_mod = require("codetyper.brain.delta.diff")
-local types = require("codetyper.brain.types")
+local storage = require("codetyper.core.memory.storage")
+local commit_mod = require("codetyper.core.memory.delta.commit")
+local diff_mod = require("codetyper.core.memory.delta.diff")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
@@ -17,7 +17,7 @@ M.diff = diff_mod
 ---@param trigger? string Trigger source
 ---@return string|nil Delta hash
 function M.commit(message, trigger)
-  local graph = require("codetyper.brain.graph")
+  local graph = require("codetyper.core.memory.graph")
   local changes = graph.get_pending_changes()
 
   if #changes == 0 then
@@ -87,7 +87,7 @@ end
 --- Apply changes to current state
 ---@param changes table[] Changes to apply
 function M.apply_changes(changes)
-  local node_mod = require("codetyper.brain.graph.node")
+  local node_mod = require("codetyper.core.memory.graph.node")
 
   for _, change in ipairs(changes) do
     local parts = vim.split(change.path, ".", { plain = true })
@@ -117,7 +117,7 @@ function M.apply_changes(changes)
       end
     elseif parts[1] == "graph" then
       -- Handle graph/edge changes
-      local edge_mod = require("codetyper.brain.graph.edge")
+      local edge_mod = require("codetyper.core.memory.graph.edge")
       if parts[2] == "edges" and #parts >= 3 then
         local edge_id = parts[3]
         if change.op == types.DELTA_OPS.ADD then
@@ -168,17 +168,17 @@ end
 --- Check if there are uncommitted changes
 ---@return boolean
 function M.has_pending()
-  local graph = require("codetyper.brain.graph")
-  local node_pending = require("codetyper.brain.graph.node").pending
-  local edge_pending = require("codetyper.brain.graph.edge").pending
+  local graph = require("codetyper.core.memory.graph")
+  local node_pending = require("codetyper.core.memory.graph.node").pending
+  local edge_pending = require("codetyper.core.memory.graph.edge").pending
   return #node_pending > 0 or #edge_pending > 0
 end
 
 --- Get status (like git status)
 ---@return table Status info
 function M.status()
-  local node_pending = require("codetyper.brain.graph.node").pending
-  local edge_pending = require("codetyper.brain.graph.edge").pending
+  local node_pending = require("codetyper.core.memory.graph.node").pending
+  local edge_pending = require("codetyper.core.memory.graph.edge").pending
 
   local adds = 0
   local mods = 0
@@ -268,8 +268,8 @@ function M.reset()
   })
 
   -- Clear pending
-  require("codetyper.brain.graph.node").pending = {}
-  require("codetyper.brain.graph.edge").pending = {}
+  require("codetyper.core.memory.graph.node").pending = {}
+  require("codetyper.core.memory.graph.edge").pending = {}
 
   storage.flush_all()
   return true
diff --git a/lua/codetyper/brain/graph/edge.lua b/lua/codetyper/core/memory/graph/edge.lua
similarity index 98%
rename from lua/codetyper/brain/graph/edge.lua
rename to lua/codetyper/core/memory/graph/edge.lua
index 0b81c92..026b2f0 100644
--- a/lua/codetyper/brain/graph/edge.lua
+++ b/lua/codetyper/core/memory/graph/edge.lua
@@ -1,9 +1,9 @@
 --- Brain Graph Edge Operations
 --- CRUD operations for node connections
 
-local storage = require("codetyper.brain.storage")
-local hash = require("codetyper.brain.hash")
-local types = require("codetyper.brain.types")
+local storage = require("codetyper.core.memory.storage")
+local hash = require("codetyper.core.memory.hash")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
diff --git a/lua/codetyper/brain/graph/init.lua b/lua/codetyper/core/memory/graph/init.lua
similarity index 94%
rename from lua/codetyper/brain/graph/init.lua
rename to lua/codetyper/core/memory/graph/init.lua
index 004652c..d31dcc6 100644
--- a/lua/codetyper/brain/graph/init.lua
+++ b/lua/codetyper/core/memory/graph/init.lua
@@ -1,11 +1,11 @@
 --- Brain Graph Coordinator
 --- High-level graph operations
 
-local node = require("codetyper.brain.graph.node")
-local edge = require("codetyper.brain.graph.edge")
-local query = require("codetyper.brain.graph.query")
-local storage = require("codetyper.brain.storage")
-local types = require("codetyper.brain.types")
+local node = require("codetyper.core.memory.graph.node")
+local edge = require("codetyper.core.memory.graph.edge")
+local query = require("codetyper.core.memory.graph.query")
+local storage = require("codetyper.core.memory.storage")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
diff --git a/lua/codetyper/brain/graph/node.lua b/lua/codetyper/core/memory/graph/node.lua
similarity index 98%
rename from lua/codetyper/brain/graph/node.lua
rename to lua/codetyper/core/memory/graph/node.lua
index eb30ec6..83606da 100644
--- a/lua/codetyper/brain/graph/node.lua
+++ b/lua/codetyper/core/memory/graph/node.lua
@@ -1,9 +1,9 @@
 --- Brain Graph Node Operations
 --- CRUD operations for learning nodes
 
-local storage = require("codetyper.brain.storage")
-local hash = require("codetyper.brain.hash")
-local types = require("codetyper.brain.types")
+local storage = require("codetyper.core.memory.storage")
+local hash = require("codetyper.core.memory.hash")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
diff --git a/lua/codetyper/brain/graph/query.lua b/lua/codetyper/core/memory/graph/query.lua
similarity index 98%
rename from lua/codetyper/brain/graph/query.lua
rename to lua/codetyper/core/memory/graph/query.lua
index b685c58..1761c80 100644
--- a/lua/codetyper/brain/graph/query.lua
+++ b/lua/codetyper/core/memory/graph/query.lua
@@ -1,18 +1,18 @@
 --- Brain Graph Query Engine
 --- Multi-dimensional traversal and relevance scoring
 
-local storage = require("codetyper.brain.storage")
-local types = require("codetyper.brain.types")
+local storage = require("codetyper.core.memory.storage")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
 --- Lazy load dependencies to avoid circular requires
 local function get_node_module()
-  return require("codetyper.brain.graph.node")
+  return require("codetyper.core.memory.graph.node")
 end
 
 local function get_edge_module()
-  return require("codetyper.brain.graph.edge")
+  return require("codetyper.core.memory.graph.edge")
 end
 
 --- Compute text similarity (simple keyword matching)
diff --git a/lua/codetyper/brain/hash.lua b/lua/codetyper/core/memory/hash.lua
similarity index 100%
rename from lua/codetyper/brain/hash.lua
rename to lua/codetyper/core/memory/hash.lua
diff --git a/lua/codetyper/brain/init.lua b/lua/codetyper/core/memory/init.lua
similarity index 91%
rename from lua/codetyper/brain/init.lua
rename to lua/codetyper/core/memory/init.lua
index 863ea30..86a0940 100644
--- a/lua/codetyper/brain/init.lua
+++ b/lua/codetyper/core/memory/init.lua
@@ -1,8 +1,8 @@
 --- Brain Learning System
 --- Graph-based knowledge storage with delta versioning
 
-local storage = require("codetyper.brain.storage")
-local types = require("codetyper.brain.types")
+local storage = require("codetyper.core.memory.storage")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
@@ -72,7 +72,7 @@ function M.learn(event)
     return nil
   end
 
-  local learners = require("codetyper.brain.learners")
+  local learners = require("codetyper.core.memory.learners")
   local node_id = learners.process(event)
 
   if node_id then
@@ -96,7 +96,7 @@ function M.query(opts)
     return { nodes = {}, edges = {}, stats = {}, truncated = false }
   end
 
-  local query_engine = require("codetyper.brain.graph.query")
+  local query_engine = require("codetyper.core.memory.graph.query")
   return query_engine.execute(opts)
 end
 
@@ -112,7 +112,7 @@ function M.get_context_for_llm(opts)
   opts.max_tokens = opts.max_tokens or config.output.max_tokens
 
   local result = M.query(opts)
-  local formatter = require("codetyper.brain.output.formatter")
+  local formatter = require("codetyper.core.memory.output.formatter")
 
   if config.output.format == "json" then
     return formatter.to_json(result, opts)
@@ -129,7 +129,7 @@ function M.commit(message)
     return nil
   end
 
-  local delta_mgr = require("codetyper.brain.delta")
+  local delta_mgr = require("codetyper.core.memory.delta")
   return delta_mgr.commit(message)
 end
 
@@ -141,7 +141,7 @@ function M.rollback(delta_hash)
     return false
   end
 
-  local delta_mgr = require("codetyper.brain.delta")
+  local delta_mgr = require("codetyper.core.memory.delta")
   return delta_mgr.rollback(delta_hash)
 end
 
@@ -153,7 +153,7 @@ function M.get_history(limit)
     return {}
   end
 
-  local delta_mgr = require("codetyper.brain.delta")
+  local delta_mgr = require("codetyper.core.memory.delta")
   return delta_mgr.get_history(limit or 50)
 end
 
@@ -170,7 +170,7 @@ function M.prune(opts)
     unused_days = config.prune.unused_days,
   }, opts or {})
 
-  local graph = require("codetyper.brain.graph")
+  local graph = require("codetyper.core.memory.graph")
   return graph.prune(opts)
 end
 
diff --git a/lua/codetyper/brain/learners/convention.lua b/lua/codetyper/core/memory/learners/convention.lua
similarity index 99%
rename from lua/codetyper/brain/learners/convention.lua
rename to lua/codetyper/core/memory/learners/convention.lua
index 9e8f097..3f1c139 100644
--- a/lua/codetyper/brain/learners/convention.lua
+++ b/lua/codetyper/core/memory/learners/convention.lua
@@ -1,7 +1,7 @@
 --- Brain Convention Learner
 --- Learns project conventions and coding standards
 
-local types = require("codetyper.brain.types")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
diff --git a/lua/codetyper/brain/learners/correction.lua b/lua/codetyper/core/memory/learners/correction.lua
similarity index 99%
rename from lua/codetyper/brain/learners/correction.lua
rename to lua/codetyper/core/memory/learners/correction.lua
index 9a94f2a..42c3677 100644
--- a/lua/codetyper/brain/learners/correction.lua
+++ b/lua/codetyper/core/memory/learners/correction.lua
@@ -1,7 +1,7 @@
 --- Brain Correction Learner
 --- Learns from user corrections and edits
 
-local types = require("codetyper.brain.types")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
diff --git a/lua/codetyper/brain/learners/init.lua b/lua/codetyper/core/memory/learners/init.lua
similarity index 93%
rename from lua/codetyper/brain/learners/init.lua
rename to lua/codetyper/core/memory/learners/init.lua
index 936313e..3291126 100644
--- a/lua/codetyper/brain/learners/init.lua
+++ b/lua/codetyper/core/memory/learners/init.lua
@@ -1,21 +1,21 @@
 --- Brain Learners Coordinator
 --- Routes learning events to appropriate learners
 
-local types = require("codetyper.brain.types")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
 -- Lazy load learners
 local function get_pattern_learner()
-  return require("codetyper.brain.learners.pattern")
+  return require("codetyper.core.memory.learners.pattern")
 end
 
 local function get_correction_learner()
-  return require("codetyper.brain.learners.correction")
+  return require("codetyper.core.memory.learners.correction")
 end
 
 local function get_convention_learner()
-  return require("codetyper.brain.learners.convention")
+  return require("codetyper.core.memory.learners.convention")
 end
 
 --- All available learners
@@ -99,7 +99,7 @@ function M.create_learning(learner, data, event)
   local params = learner.create_node_params(data)
 
   -- Get graph module
-  local graph = require("codetyper.brain.graph")
+  local graph = require("codetyper.core.memory.graph")
 
   -- Find related nodes
   local related_ids = {}
@@ -125,7 +125,7 @@ end
 ---@return string|nil Created node ID
 function M.process_feedback(event)
   local data = event.data or {}
-  local graph = require("codetyper.brain.graph")
+  local graph = require("codetyper.core.memory.graph")
 
   local content = {
     s = "Feedback: " .. (data.feedback or "unknown"),
@@ -167,7 +167,7 @@ end
 ---@return string|nil Created node ID
 function M.process_session(event)
   local data = event.data or {}
-  local graph = require("codetyper.brain.graph")
+  local graph = require("codetyper.core.memory.graph")
 
   local content = {
     s = event.type == "session_start" and "Session started" or "Session ended",
diff --git a/lua/codetyper/brain/learners/pattern.lua b/lua/codetyper/core/memory/learners/pattern.lua
similarity index 98%
rename from lua/codetyper/brain/learners/pattern.lua
rename to lua/codetyper/core/memory/learners/pattern.lua
index eabbb57..c9b09e1 100644
--- a/lua/codetyper/brain/learners/pattern.lua
+++ b/lua/codetyper/core/memory/learners/pattern.lua
@@ -1,7 +1,7 @@
 --- Brain Pattern Learner
 --- Detects and learns code patterns
 
-local types = require("codetyper.brain.types")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
diff --git a/lua/codetyper/brain/output/formatter.lua b/lua/codetyper/core/memory/output/formatter.lua
similarity index 99%
rename from lua/codetyper/brain/output/formatter.lua
rename to lua/codetyper/core/memory/output/formatter.lua
index 6a627ea..0919dbe 100644
--- a/lua/codetyper/brain/output/formatter.lua
+++ b/lua/codetyper/core/memory/output/formatter.lua
@@ -1,7 +1,7 @@
 --- Brain Output Formatter
 --- LLM-optimized output formatting
 
-local types = require("codetyper.brain.types")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
diff --git a/lua/codetyper/brain/output/init.lua b/lua/codetyper/core/memory/output/init.lua
similarity index 94%
rename from lua/codetyper/brain/output/init.lua
rename to lua/codetyper/core/memory/output/init.lua
index 1009561..b484c6d 100644
--- a/lua/codetyper/brain/output/init.lua
+++ b/lua/codetyper/core/memory/output/init.lua
@@ -1,7 +1,7 @@
 --- Brain Output Coordinator
 --- Manages LLM context generation
 
-local formatter = require("codetyper.brain.output.formatter")
+local formatter = require("codetyper.core.memory.output.formatter")
 
 local M = {}
 
@@ -17,7 +17,7 @@ local DEFAULT_MAX_TOKENS = 4000
 function M.generate(opts)
   opts = opts or {}
 
-  local brain = require("codetyper.brain")
+  local brain = require("codetyper.core.memory")
   if not brain.is_initialized() then
     return ""
   end
@@ -138,7 +138,7 @@ end
 --- Check if context is available
 ---@return boolean
 function M.has_context()
-  local brain = require("codetyper.brain")
+  local brain = require("codetyper.core.memory")
   if not brain.is_initialized() then
     return false
   end
@@ -150,7 +150,7 @@ end
 --- Get context stats
 ---@return table Stats
 function M.stats()
-  local brain = require("codetyper.brain")
+  local brain = require("codetyper.core.memory")
   if not brain.is_initialized() then
     return { available = false }
   end
diff --git a/lua/codetyper/brain/storage.lua b/lua/codetyper/core/memory/storage.lua
similarity index 98%
rename from lua/codetyper/brain/storage.lua
rename to lua/codetyper/core/memory/storage.lua
index 6433f7b..8f776dc 100644
--- a/lua/codetyper/brain/storage.lua
+++ b/lua/codetyper/core/memory/storage.lua
@@ -1,8 +1,8 @@
 --- Brain Storage Layer
 --- Cache + disk persistence with lazy loading
 
-local utils = require("codetyper.utils")
-local types = require("codetyper.brain.types")
+local utils = require("codetyper.support.utils")
+local types = require("codetyper.core.memory.types")
 
 local M = {}
 
diff --git a/lua/codetyper/brain/types.lua b/lua/codetyper/core/memory/types.lua
similarity index 100%
rename from lua/codetyper/brain/types.lua
rename to lua/codetyper/core/memory/types.lua
diff --git a/lua/codetyper/agent/executor.lua b/lua/codetyper/core/scheduler/executor.lua
similarity index 99%
rename from lua/codetyper/agent/executor.lua
rename to lua/codetyper/core/scheduler/executor.lua
index 32e8ef7..ddb5d32 100644
--- a/lua/codetyper/agent/executor.lua
+++ b/lua/codetyper/core/scheduler/executor.lua
@@ -3,8 +3,8 @@
 --- Executes tools requested by the LLM and returns results.
 
 local M = {}
-local utils = require("codetyper.utils")
-local logs = require("codetyper.agent.logs")
+local utils = require("codetyper.support.utils")
+local logs = require("codetyper.adapters.nvim.ui.logs")
 
 ---@class ExecutionResult
 ---@field success boolean Whether the execution succeeded
diff --git a/lua/codetyper/agent/loop.lua b/lua/codetyper/core/scheduler/loop.lua
similarity index 97%
rename from lua/codetyper/agent/loop.lua
rename to lua/codetyper/core/scheduler/loop.lua
index afba6a7..1889b18 100644
--- a/lua/codetyper/agent/loop.lua
+++ b/lua/codetyper/core/scheduler/loop.lua
@@ -144,8 +144,8 @@ end
 --- Execute the agent loop
 ---@param opts AgentLoopOpts
 function M.run(opts)
-	local tools_mod = require("codetyper.agent.tools")
-	local llm = require("codetyper.llm")
+	local tools_mod = require("codetyper.core.tools")
+	local llm = require("codetyper.core.llm")
 
 	-- Get tools
 	local tools = opts.tools or tools_mod.list()
@@ -280,7 +280,7 @@ function M.run(opts)
 						local tool_opts = {
 							on_log = function(msg)
 								pcall(function()
-									local logs = require("codetyper.agent.logs")
+									local logs = require("codetyper.adapters.nvim.ui.logs")
 									logs.add({ type = "tool", message = msg })
 								end)
 							end,
@@ -363,7 +363,7 @@ function M.dispatch(prompt, on_complete, opts)
 	opts = opts or {}
 
 	-- Sub-agents get limited tools by default
-	local tools_mod = require("codetyper.agent.tools")
+	local tools_mod = require("codetyper.core.tools")
 	local safe_tools = tools_mod.list(function(tool)
 		return tool.name == "view" or tool.name == "grep" or tool.name == "glob"
 	end)
diff --git a/lua/codetyper/agent/resume.lua b/lua/codetyper/core/scheduler/resume.lua
similarity index 98%
rename from lua/codetyper/agent/resume.lua
rename to lua/codetyper/core/scheduler/resume.lua
index ef44dd5..fcf3052 100644
--- a/lua/codetyper/agent/resume.lua
+++ b/lua/codetyper/core/scheduler/resume.lua
@@ -4,7 +4,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Get the resume context directory
 ---@return string|nil
diff --git a/lua/codetyper/agent/scheduler.lua b/lua/codetyper/core/scheduler/scheduler.lua
similarity index 95%
rename from lua/codetyper/agent/scheduler.lua
rename to lua/codetyper/core/scheduler/scheduler.lua
index a344154..4c5b8ce 100644
--- a/lua/codetyper/agent/scheduler.lua
+++ b/lua/codetyper/core/scheduler/scheduler.lua
@@ -6,11 +6,11 @@
 
 local M = {}
 
-local queue = require("codetyper.agent.queue")
-local patch = require("codetyper.agent.patch")
-local worker = require("codetyper.agent.worker")
-local confidence_mod = require("codetyper.agent.confidence")
-local context_modal = require("codetyper.agent.context_modal")
+local queue = require("codetyper.core.events.queue")
+local patch = require("codetyper.core.diff.patch")
+local worker = require("codetyper.core.scheduler.worker")
+local confidence_mod = require("codetyper.core.llm.confidence")
+local context_modal = require("codetyper.adapters.nvim.ui.context_modal")
 local params = require("codetyper.params.agent.scheduler")
 
 -- Setup context modal cleanup on exit
@@ -138,7 +138,7 @@ local function retry_with_context(original_event, additional_context, attached_f
 
 	-- Log the retry
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "info",
 			message = string.format("Retrying with additional context (original: %s)", original_event.id),
@@ -229,7 +229,7 @@ local function handle_worker_result(event, result)
 	-- Check if LLM needs more context
 	if result.needs_context then
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.add({
 				type = "info",
 				message = string.format("Event %s: LLM needs more context, opening modal", event.id),
@@ -285,7 +285,7 @@ local function handle_worker_result(event, result)
 		end
 		if requested and #requested > 0 then
 			pcall(function()
-				local logs = require("codetyper.agent.logs")
+				local logs = require("codetyper.adapters.nvim.ui.logs")
 				logs.add({ type = "info", message = string.format("Auto-attaching %d requested file(s)", #requested) })
 			end)
 
@@ -328,7 +328,7 @@ local function handle_worker_result(event, result)
 		-- Failed - try escalation if this was ollama
 		if result.worker_type == "ollama" and event.attempt_count < 2 then
 			pcall(function()
-				local logs = require("codetyper.agent.logs")
+				local logs = require("codetyper.adapters.nvim.ui.logs")
 				logs.add({
 					type = "info",
 					message = string.format(
@@ -358,7 +358,7 @@ local function handle_worker_result(event, result)
 	if needs_escalation and result.worker_type == "ollama" and event.attempt_count < 2 then
 		-- Low confidence from ollama - escalate to remote
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.add({
 				type = "info",
 				message = string.format(
@@ -383,7 +383,7 @@ local function handle_worker_result(event, result)
 	-- Schedule patch application after delay (gives user time to review/cancel)
 	local delay = state.config.apply_delay_ms or 5000
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "info",
 			message = string.format("Code ready. Applying in %.1f seconds...", delay / 1000),
@@ -416,7 +416,7 @@ local function dispatch_next()
 	local should_skip, skip_reason = queue.check_precedence(event)
 	if should_skip then
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.add({
 				type = "warning",
 				message = string.format("Event %s skipped: %s", event.id, skip_reason or "conflict"),
@@ -432,7 +432,7 @@ local function dispatch_next()
 
 	-- Log dispatch with intent/scope info
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		local intent_info = event.intent and event.intent.type or "unknown"
 		local scope_info = event.scope and event.scope.type ~= "file"
 			and string.format("%s:%s", event.scope.type, event.scope.name or "anon")
@@ -474,7 +474,7 @@ function M.schedule_patch_flush()
 			local applied, stale = patch.flush_pending_smart()
 			if applied > 0 or stale > 0 then
 				pcall(function()
-					local logs = require("codetyper.agent.logs")
+					local logs = require("codetyper.adapters.nvim.ui.logs")
 					logs.add({
 						type = "info",
 						message = string.format("Patches flushed: %d applied, %d stale", applied, stale),
@@ -487,7 +487,7 @@ function M.schedule_patch_flush()
 			if not waiting_to_flush then
 				waiting_to_flush = true
 				pcall(function()
-					local logs = require("codetyper.agent.logs")
+					local logs = require("codetyper.adapters.nvim.ui.logs")
 					logs.add({
 						type = "info",
 						message = "Waiting for user to finish typing before applying code...",
@@ -628,7 +628,7 @@ function M.start(config)
 	scheduler_loop()
 
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "info",
 			message = "Scheduler started",
@@ -660,7 +660,7 @@ function M.stop()
 	end
 
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "info",
 			message = "Scheduler stopped",
diff --git a/lua/codetyper/agent/worker.lua b/lua/codetyper/core/scheduler/worker.lua
similarity index 97%
rename from lua/codetyper/agent/worker.lua
rename to lua/codetyper/core/scheduler/worker.lua
index 7d520a9..7b15c66 100644
--- a/lua/codetyper/agent/worker.lua
+++ b/lua/codetyper/core/scheduler/worker.lua
@@ -7,7 +7,7 @@
 local M = {}
 
 local params = require("codetyper.params.agent.worker")
-local confidence = require("codetyper.agent.confidence")
+local confidence = require("codetyper.core.llm.confidence")
 
 ---@class WorkerResult
 ---@field success boolean Whether the request succeeded
@@ -399,7 +399,7 @@ end
 ---@return string prompt
 ---@return table context
 local function build_prompt(event)
-	local intent_mod = require("codetyper.agent.intent")
+	local intent_mod = require("codetyper.core.intent")
 
 	-- Get target file content for context
 	local target_content = ""
@@ -420,7 +420,7 @@ local function build_prompt(event)
 	local indexed_context = nil
 	local indexed_content = ""
 	pcall(function()
-		local indexer = require("codetyper.indexer")
+		local indexer = require("codetyper.features.indexer")
 		indexed_context = indexer.get_context_for({
 			file = event.target_path,
 			intent = event.intent,
@@ -439,7 +439,7 @@ local function build_prompt(event)
 	-- Get brain memories - contextual recall based on current task
 	local brain_context = ""
 	pcall(function()
-		local brain = require("codetyper.brain")
+		local brain = require("codetyper.core.memory")
 		if brain.is_initialized() then
 			-- Query brain for relevant memories based on:
 			-- 1. Current file (file-specific patterns)
@@ -726,7 +726,7 @@ function M.create(event, worker_type, callback)
 
 	-- Log worker creation
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "worker",
 			message = string.format("Worker %s started (%s)", worker.id, worker_type),
@@ -756,7 +756,7 @@ function M.start(worker)
 			active_workers[worker.id] = nil
 
 			pcall(function()
-				local logs = require("codetyper.agent.logs")
+				local logs = require("codetyper.adapters.nvim.ui.logs")
 				logs.add({
 					type = "warning",
 					message = string.format("Worker %s timed out after %dms", worker.id, worker.timeout_ms),
@@ -810,7 +810,7 @@ function M.start(worker)
 			-- Log if pondering occurred
 			if usage_or_metadata.pondered then
 				pcall(function()
-					local logs = require("codetyper.agent.logs")
+					local logs = require("codetyper.adapters.nvim.ui.logs")
 					logs.add({
 						type = "info",
 						message = string.format(
@@ -828,7 +828,7 @@ function M.start(worker)
 
 	-- Use smart selection or direct client
 	if use_smart_selection then
-		local llm = require("codetyper.llm")
+		local llm = require("codetyper.core.llm")
 		llm.smart_generate(prompt, context, handle_response)
 	else
 		-- Get client and execute directly
@@ -854,7 +854,7 @@ function M.complete(worker, response, error, usage)
 		active_workers[worker.id] = nil
 
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.add({
 				type = "error",
 				message = string.format("Worker %s failed: %s", worker.id, error),
@@ -880,7 +880,7 @@ function M.complete(worker, response, error, usage)
 		active_workers[worker.id] = nil
 
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.add({
 				type = "info",
 				message = string.format("Worker %s: LLM needs more context", worker.id),
@@ -904,7 +904,7 @@ function M.complete(worker, response, error, usage)
 
 	-- Log the full raw LLM response (for debugging)
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "response",
 			message = "--- LLM Response ---",
@@ -925,7 +925,7 @@ function M.complete(worker, response, error, usage)
 	active_workers[worker.id] = nil
 
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "success",
 			message = string.format(
@@ -972,7 +972,7 @@ function M.cancel(worker_id)
 	active_workers[worker_id] = nil
 
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "info",
 			message = string.format("Worker %s cancelled", worker_id),
diff --git a/lua/codetyper/agent/scope.lua b/lua/codetyper/core/scope/init.lua
similarity index 100%
rename from lua/codetyper/agent/scope.lua
rename to lua/codetyper/core/scope/init.lua
diff --git a/lua/codetyper/agent/tools/base.lua b/lua/codetyper/core/tools/base.lua
similarity index 100%
rename from lua/codetyper/agent/tools/base.lua
rename to lua/codetyper/core/tools/base.lua
diff --git a/lua/codetyper/agent/tools/bash.lua b/lua/codetyper/core/tools/bash.lua
similarity index 98%
rename from lua/codetyper/agent/tools/bash.lua
rename to lua/codetyper/core/tools/bash.lua
index 7421209..c5d0bbb 100644
--- a/lua/codetyper/agent/tools/bash.lua
+++ b/lua/codetyper/core/tools/bash.lua
@@ -3,7 +3,7 @@
 --- Tool for executing shell commands with safety checks.
 ---@brief ]]
 
-local Base = require("codetyper.agent.tools.base")
+local Base = require("codetyper.core.tools.base")
 local description = require("codetyper.prompts.agent.bash").description
 local params = require("codetyper.params.agent.bash").params
 local returns = require("codetyper.params.agent.bash").returns
diff --git a/lua/codetyper/agent/tools/edit.lua b/lua/codetyper/core/tools/edit.lua
similarity index 99%
rename from lua/codetyper/agent/tools/edit.lua
rename to lua/codetyper/core/tools/edit.lua
index 8a485f2..dfac9b2 100644
--- a/lua/codetyper/agent/tools/edit.lua
+++ b/lua/codetyper/core/tools/edit.lua
@@ -5,7 +5,7 @@
 --- Multi-strategy approach for reliable editing.
 ---@brief ]]
 
-local Base = require("codetyper.agent.tools.base")
+local Base = require("codetyper.core.tools.base")
 local description = require("codetyper.prompts.agent.edit").description
 local params = require("codetyper.params.agent.edit").params
 local returns = require("codetyper.params.agent.edit").returns
diff --git a/lua/codetyper/agent/tools/glob.lua b/lua/codetyper/core/tools/glob.lua
similarity index 98%
rename from lua/codetyper/agent/tools/glob.lua
rename to lua/codetyper/core/tools/glob.lua
index 7ede066..3355f1f 100644
--- a/lua/codetyper/agent/tools/glob.lua
+++ b/lua/codetyper/core/tools/glob.lua
@@ -3,7 +3,7 @@
 --- Tool for finding files by glob pattern.
 ---@brief ]]
 
-local Base = require("codetyper.agent.tools.base")
+local Base = require("codetyper.core.tools.base")
 
 ---@class CoderTool
 local M = setmetatable({}, Base)
diff --git a/lua/codetyper/agent/tools/grep.lua b/lua/codetyper/core/tools/grep.lua
similarity index 97%
rename from lua/codetyper/agent/tools/grep.lua
rename to lua/codetyper/core/tools/grep.lua
index 1f34b97..b16afed 100644
--- a/lua/codetyper/agent/tools/grep.lua
+++ b/lua/codetyper/core/tools/grep.lua
@@ -3,7 +3,7 @@
 --- Tool for searching file contents using ripgrep.
 ---@brief ]]
 
-local Base = require("codetyper.agent.tools.base")
+local Base = require("codetyper.core.tools.base")
 local description = require("codetyper.params.agent.grep").description
 local params = require("codetyper.prompts.agents.grep").params
 local returns = require("codetyper.prompts.agents.grep").returns
diff --git a/lua/codetyper/agent/tools.lua b/lua/codetyper/core/tools/init.lua
similarity index 100%
rename from lua/codetyper/agent/tools.lua
rename to lua/codetyper/core/tools/init.lua
diff --git a/lua/codetyper/agent/tools/init.lua b/lua/codetyper/core/tools/registry.lua
similarity index 95%
rename from lua/codetyper/agent/tools/init.lua
rename to lua/codetyper/core/tools/registry.lua
index d6259ca..fddfa88 100644
--- a/lua/codetyper/agent/tools/init.lua
+++ b/lua/codetyper/core/tools/registry.lua
@@ -162,27 +162,27 @@ end
 --- Load built-in tools
 function M.load_builtins()
 	-- View file tool
-	local view = require("codetyper.agent.tools.view")
+	local view = require("codetyper.core.tools.view")
 	M.register(view)
 
 	-- Bash tool
-	local bash = require("codetyper.agent.tools.bash")
+	local bash = require("codetyper.core.tools.bash")
 	M.register(bash)
 
 	-- Grep tool
-	local grep = require("codetyper.agent.tools.grep")
+	local grep = require("codetyper.core.tools.grep")
 	M.register(grep)
 
 	-- Glob tool
-	local glob = require("codetyper.agent.tools.glob")
+	local glob = require("codetyper.core.tools.glob")
 	M.register(glob)
 
 	-- Write file tool
-	local write = require("codetyper.agent.tools.write")
+	local write = require("codetyper.core.tools.write")
 	M.register(write)
 
 	-- Edit tool
-	local edit = require("codetyper.agent.tools.edit")
+	local edit = require("codetyper.core.tools.edit")
 	M.register(edit)
 end
 
diff --git a/lua/codetyper/agent/tools/view.lua b/lua/codetyper/core/tools/view.lua
similarity index 98%
rename from lua/codetyper/agent/tools/view.lua
rename to lua/codetyper/core/tools/view.lua
index a3eb641..a7251da 100644
--- a/lua/codetyper/agent/tools/view.lua
+++ b/lua/codetyper/core/tools/view.lua
@@ -3,7 +3,7 @@
 --- Tool for reading file contents with line range support.
 ---@brief ]]
 
-local Base = require("codetyper.agent.tools.base")
+local Base = require("codetyper.core.tools.base")
 
 ---@class CoderTool
 local M = setmetatable({}, Base)
diff --git a/lua/codetyper/agent/tools/write.lua b/lua/codetyper/core/tools/write.lua
similarity index 96%
rename from lua/codetyper/agent/tools/write.lua
rename to lua/codetyper/core/tools/write.lua
index 946a1bb..1480a84 100644
--- a/lua/codetyper/agent/tools/write.lua
+++ b/lua/codetyper/core/tools/write.lua
@@ -3,7 +3,7 @@
 --- Tool for creating or overwriting files.
 ---@brief ]]
 
-local Base = require("codetyper.agent.tools.base")
+local Base = require("codetyper.core.tools.base")
 local description = require("codetyper.prompts.agents.write").description
 local params = require("codetyper.params.agents.write")
 
diff --git a/lua/codetyper/agent/context_builder.lua b/lua/codetyper/features/agents/context_builder.lua
similarity index 99%
rename from lua/codetyper/agent/context_builder.lua
rename to lua/codetyper/features/agents/context_builder.lua
index 4e1df44..62ad83b 100644
--- a/lua/codetyper/agent/context_builder.lua
+++ b/lua/codetyper/features/agents/context_builder.lua
@@ -5,7 +5,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 local params = require("codetyper.params.agent.context")
 
 --- Get project structure as a tree string
diff --git a/lua/codetyper/agent/agentic.lua b/lua/codetyper/features/agents/engine.lua
similarity index 97%
rename from lua/codetyper/agent/agentic.lua
rename to lua/codetyper/features/agents/engine.lua
index 6164555..f67c288 100644
--- a/lua/codetyper/agent/agentic.lua
+++ b/lua/codetyper/features/agents/engine.lua
@@ -31,7 +31,7 @@ local M = {}
 ---@field on_complete? fun(result: string|nil, error: string|nil) Called when done
 ---@field on_status? fun(status: string) Status updates
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Load agent definition
 ---@param name string Agent name
@@ -177,7 +177,7 @@ end
 ---@param provider string "openai"|"claude"
 ---@return table[] Formatted tools
 local function build_tools(tool_names, provider)
-	local tools_mod = require("codetyper.agent.tools")
+	local tools_mod = require("codetyper.core.tools")
 	local tools = {}
 
 	for _, name in ipairs(tool_names) do
@@ -234,7 +234,7 @@ end
 ---@return string result
 ---@return string|nil error
 local function execute_tool(tool_call, opts)
-	local tools_mod = require("codetyper.agent.tools")
+	local tools_mod = require("codetyper.core.tools")
 	local name = tool_call["function"].name
 	local args = tool_call["function"].arguments
 
@@ -363,7 +363,7 @@ local function call_llm(messages, tools, system_prompt, provider, model, callbac
 
 	-- Use native tool calling APIs
 	if provider == "copilot" then
-		local client = require("codetyper.llm.copilot")
+		local client = require("codetyper.core.llm.copilot")
 
 		-- Copilot's generate_with_tools expects messages in a specific format
 		-- Convert to the format it expects
@@ -406,7 +406,7 @@ local function call_llm(messages, tools, system_prompt, provider, model, callbac
 			callback(result, nil)
 		end)
 	elseif provider == "openai" then
-		local client = require("codetyper.llm.openai")
+		local client = require("codetyper.core.llm.openai")
 
 		-- OpenAI's generate_with_tools
 		local converted_messages = {}
@@ -447,7 +447,7 @@ local function call_llm(messages, tools, system_prompt, provider, model, callbac
 			callback(result, nil)
 		end)
 	elseif provider == "ollama" then
-		local client = require("codetyper.llm.ollama")
+		local client = require("codetyper.core.llm.ollama")
 
 		-- Ollama's generate_with_tools (text-based tool calling)
 		local converted_messages = {}
@@ -468,7 +468,7 @@ local function call_llm(messages, tools, system_prompt, provider, model, callbac
 		end)
 	else
 		-- Fallback for other providers (ollama, etc.) - use text-based parsing
-		local client = require("codetyper.llm." .. provider)
+		local client = require("codetyper.core.llm." .. provider)
 
 		-- Build prompt from messages
 		local prompts = require("codetyper.prompts.agent")
@@ -578,7 +578,7 @@ function M.run(opts)
 	local tool_names = agent.tools or { "view", "edit", "write", "grep", "glob", "bash" }
 
 	-- Ensure tools are loaded
-	local tools_mod = require("codetyper.agent.tools")
+	local tools_mod = require("codetyper.core.tools")
 	tools_mod.setup()
 
 	-- Build tools for API
diff --git a/lua/codetyper/agent/init.lua b/lua/codetyper/features/agents/init.lua
similarity index 96%
rename from lua/codetyper/agent/init.lua
rename to lua/codetyper/features/agents/init.lua
index 1bc001f..858f15c 100644
--- a/lua/codetyper/agent/init.lua
+++ b/lua/codetyper/features/agents/init.lua
@@ -4,14 +4,14 @@
 
 local M = {}
 
-local tools = require("codetyper.agent.tools")
-local executor = require("codetyper.agent.executor")
-local parser = require("codetyper.agent.parser")
-local diff = require("codetyper.agent.diff")
-local diff_review = require("codetyper.agent.diff_review")
-local resume = require("codetyper.agent.resume")
-local utils = require("codetyper.utils")
-local logs = require("codetyper.agent.logs")
+local tools = require("codetyper.core.tools")
+local executor = require("codetyper.core.scheduler.executor")
+local parser = require("codetyper.core.llm.parser")
+local diff = require("codetyper.core.diff.diff")
+local diff_review = require("codetyper.adapters.nvim.ui.diff_review")
+local resume = require("codetyper.core.scheduler.resume")
+local utils = require("codetyper.support.utils")
+local logs = require("codetyper.adapters.nvim.ui.logs")
 
 ---@class AgentState
 ---@field conversation table[] Message history for multi-turn
@@ -107,7 +107,7 @@ function M.agent_loop(context, callbacks)
     return
   end
 
-  local llm = require("codetyper.llm")
+  local llm = require("codetyper.core.llm")
   local client = llm.get_client()
 
   -- Check if client supports tools
@@ -416,7 +416,7 @@ function M.continue_session(callbacks)
   state.current_callbacks = callbacks
 
   -- Build context from current state
-  local llm = require("codetyper.llm")
+  local llm = require("codetyper.core.llm")
   local context = {}
   local current_file = vim.fn.expand("%:p")
   if current_file ~= "" and vim.fn.filereadable(current_file) == 1 then
diff --git a/lua/codetyper/agent/linter.lua b/lua/codetyper/features/agents/linter.lua
similarity index 96%
rename from lua/codetyper/agent/linter.lua
rename to lua/codetyper/features/agents/linter.lua
index 1355126..b9afcb1 100644
--- a/lua/codetyper/agent/linter.lua
+++ b/lua/codetyper/features/agents/linter.lua
@@ -60,7 +60,7 @@ local function save_buffer(bufnr)
 
 	if not ok then
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.add({
 				type = "warning",
 				message = "Failed to save buffer: " .. tostring(err),
@@ -185,7 +185,7 @@ function M.validate_after_injection(bufnr, start_line, end_line, callback)
 
 		-- Log results
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			if result.has_errors then
 				logs.add({
 					type = "error",
@@ -332,9 +332,9 @@ function M.request_ai_fix(bufnr, result)
 	)
 
 	-- Queue the fix through the scheduler
-	local scheduler = require("codetyper.agent.scheduler")
-	local queue = require("codetyper.agent.queue")
-	local patch_mod = require("codetyper.agent.patch")
+	local scheduler = require("codetyper.core.scheduler.scheduler")
+	local queue = require("codetyper.core.events.queue")
+	local patch_mod = require("codetyper.core.diff.patch")
 
 	-- Ensure scheduler is running
 	if not scheduler.status().running then
@@ -370,7 +370,7 @@ function M.request_ai_fix(bufnr, result)
 	})
 
 	pcall(function()
-		local logs = require("codetyper.agent.logs")
+		local logs = require("codetyper.adapters.nvim.ui.logs")
 		logs.add({
 			type = "info",
 			message = "Queued AI fix request for lint errors",
diff --git a/lua/codetyper/agent/permissions.lua b/lua/codetyper/features/agents/permissions.lua
similarity index 100%
rename from lua/codetyper/agent/permissions.lua
rename to lua/codetyper/features/agents/permissions.lua
diff --git a/lua/codetyper/ask.lua b/lua/codetyper/features/ask/engine.lua
similarity index 99%
rename from lua/codetyper/ask.lua
rename to lua/codetyper/features/ask/engine.lua
index 16c8962..c7458e3 100644
--- a/lua/codetyper/ask.lua
+++ b/lua/codetyper/features/ask/engine.lua
@@ -2,7 +2,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 ---@class AskState
 ---@field input_buf number|nil Input buffer
@@ -345,7 +345,7 @@ local function setup_log_listener()
 	-- Remove existing listener if any
 	if state.log_listener_id then
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.remove_listener(state.log_listener_id)
 		end)
 		state.log_listener_id = nil
@@ -362,7 +362,7 @@ end
 local function remove_log_listener()
 	if state.log_listener_id then
 		pcall(function()
-			local logs = require("codetyper.agent.logs")
+			local logs = require("codetyper.adapters.nvim.ui.logs")
 			logs.remove_listener(state.log_listener_id)
 		end)
 		state.log_listener_id = nil
diff --git a/lua/codetyper/ask/explorer.lua b/lua/codetyper/features/ask/explorer.lua
similarity index 99%
rename from lua/codetyper/ask/explorer.lua
rename to lua/codetyper/features/ask/explorer.lua
index cc03f4a..8c199ce 100644
--- a/lua/codetyper/ask/explorer.lua
+++ b/lua/codetyper/features/ask/explorer.lua
@@ -6,7 +6,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 ---@class ExplorationState
 ---@field is_exploring boolean
diff --git a/lua/codetyper/ask/intent.lua b/lua/codetyper/features/ask/intent.lua
similarity index 100%
rename from lua/codetyper/ask/intent.lua
rename to lua/codetyper/features/ask/intent.lua
diff --git a/lua/codetyper/agent/inject.lua b/lua/codetyper/features/completion/inject.lua
similarity index 99%
rename from lua/codetyper/agent/inject.lua
rename to lua/codetyper/features/completion/inject.lua
index e2bdbc5..8ff4f9c 100644
--- a/lua/codetyper/agent/inject.lua
+++ b/lua/codetyper/features/completion/inject.lua
@@ -17,7 +17,7 @@ local M = {}
 ---@field body string[] Non-import code lines
 ---@field import_lines table<number, boolean> Map of line numbers that are imports
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 local languages = require("codetyper.params.agent.languages")
 local import_patterns = languages.import_patterns
 
diff --git a/lua/codetyper/completion.lua b/lua/codetyper/features/completion/inline.lua
similarity index 99%
rename from lua/codetyper/completion.lua
rename to lua/codetyper/features/completion/inline.lua
index c66f39b..a4fbf97 100644
--- a/lua/codetyper/completion.lua
+++ b/lua/codetyper/features/completion/inline.lua
@@ -5,7 +5,7 @@
 local M = {}
 
 local parser = require("codetyper.parser")
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Get list of files for completion
 ---@param prefix string Prefix to filter files
diff --git a/lua/codetyper/suggestion/init.lua b/lua/codetyper/features/completion/suggestion.lua
similarity index 100%
rename from lua/codetyper/suggestion/init.lua
rename to lua/codetyper/features/completion/suggestion.lua
diff --git a/lua/codetyper/indexer/analyzer.lua b/lua/codetyper/features/indexer/analyzer.lua
similarity index 99%
rename from lua/codetyper/indexer/analyzer.lua
rename to lua/codetyper/features/indexer/analyzer.lua
index 2babd95..dfc5de5 100644
--- a/lua/codetyper/indexer/analyzer.lua
+++ b/lua/codetyper/features/indexer/analyzer.lua
@@ -6,8 +6,8 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
-local scanner = require("codetyper.indexer.scanner")
+local utils = require("codetyper.support.utils")
+local scanner = require("codetyper.features.indexer.scanner")
 
 --- Language-specific query patterns for Tree-sitter
 local TS_QUERIES = {
diff --git a/lua/codetyper/indexer/init.lua b/lua/codetyper/features/indexer/init.lua
similarity index 96%
rename from lua/codetyper/indexer/init.lua
rename to lua/codetyper/features/indexer/init.lua
index 69a065e..4172b46 100644
--- a/lua/codetyper/indexer/init.lua
+++ b/lua/codetyper/features/indexer/init.lua
@@ -6,7 +6,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Index schema version for migrations
 local INDEX_VERSION = 1
@@ -194,8 +194,8 @@ end
 ---@param callback? fun(index: ProjectIndex)
 ---@return ProjectIndex|nil
 function M.index_project(callback)
-	local scanner = require("codetyper.indexer.scanner")
-	local analyzer = require("codetyper.indexer.analyzer")
+	local scanner = require("codetyper.features.indexer.scanner")
+	local analyzer = require("codetyper.features.indexer.analyzer")
 
 	local index = create_empty_index()
 	local root = utils.get_project_root()
@@ -256,7 +256,7 @@ function M.index_project(callback)
 	M.save_index(index)
 
 	-- Store memories
-	local memory = require("codetyper.indexer.memory")
+	local memory = require("codetyper.features.indexer.memory")
 	memory.store_index_summary(index)
 
 	-- Sync project summary to brain
@@ -331,8 +331,8 @@ end
 ---@param filepath string
 ---@return FileIndex|nil
 function M.index_file(filepath)
-	local analyzer = require("codetyper.indexer.analyzer")
-	local memory = require("codetyper.indexer.memory")
+	local analyzer = require("codetyper.features.indexer.analyzer")
+	local memory = require("codetyper.features.indexer.memory")
 	local root = utils.get_project_root()
 
 	if not root then
@@ -475,7 +475,7 @@ function M.schedule_index_file(filepath)
 	end
 
 	-- Check if file should be indexed
-	local scanner = require("codetyper.indexer.scanner")
+	local scanner = require("codetyper.features.indexer.scanner")
 	if not scanner.should_index(filepath, config) then
 		return
 	end
@@ -496,7 +496,7 @@ end
 ---@param opts {file: string, intent: table|nil, prompt: string, scope: string|nil}
 ---@return table Context information
 function M.get_context_for(opts)
-	local memory = require("codetyper.indexer.memory")
+	local memory = require("codetyper.features.indexer.memory")
 	local index = M.load_index()
 
 	local context = {
diff --git a/lua/codetyper/indexer/memory.lua b/lua/codetyper/features/indexer/memory.lua
similarity index 99%
rename from lua/codetyper/indexer/memory.lua
rename to lua/codetyper/features/indexer/memory.lua
index 9b45cbc..e020623 100644
--- a/lua/codetyper/indexer/memory.lua
+++ b/lua/codetyper/features/indexer/memory.lua
@@ -6,7 +6,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Memory directories
 local MEMORIES_DIR = "memories"
diff --git a/lua/codetyper/indexer/scanner.lua b/lua/codetyper/features/indexer/scanner.lua
similarity index 99%
rename from lua/codetyper/indexer/scanner.lua
rename to lua/codetyper/features/indexer/scanner.lua
index 1846ebf..f1a767e 100644
--- a/lua/codetyper/indexer/scanner.lua
+++ b/lua/codetyper/features/indexer/scanner.lua
@@ -5,7 +5,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Project type markers
 local PROJECT_MARKERS = {
diff --git a/lua/codetyper/init.lua b/lua/codetyper/init.lua
index 4335d07..191dbe0 100644
--- a/lua/codetyper/init.lua
+++ b/lua/codetyper/init.lua
@@ -22,16 +22,16 @@ function M.setup(opts)
     return
   end
 
-  local config = require("codetyper.config")
+  local config = require("codetyper.config.defaults")
   M.config = config.setup(opts)
 
   -- Initialize modules
-  local commands = require("codetyper.commands")
-  local gitignore = require("codetyper.gitignore")
-  local autocmds = require("codetyper.autocmds")
-  local tree = require("codetyper.tree")
-  local completion = require("codetyper.completion")
-  local logs_panel = require("codetyper.logs_panel")
+  local commands = require("codetyper.adapters.nvim.commands")
+  local gitignore = require("codetyper.support.gitignore")
+  local autocmds = require("codetyper.adapters.nvim.autocmds")
+  local tree = require("codetyper.support.tree")
+  local completion = require("codetyper.features.completion.inline")
+  local logs_panel = require("codetyper.adapters.nvim.ui.logs_panel")
 
   -- Register commands
   commands.setup()
@@ -53,25 +53,25 @@ function M.setup(opts)
 
   -- Initialize project indexer if enabled
   if M.config.indexer and M.config.indexer.enabled then
-    local indexer = require("codetyper.indexer")
+    local indexer = require("codetyper.features.indexer")
     indexer.setup(M.config.indexer)
   end
 
   -- Initialize brain learning system if enabled
   if M.config.brain and M.config.brain.enabled then
-    local brain = require("codetyper.brain")
+    local brain = require("codetyper.core.memory")
     brain.setup(M.config.brain)
   end
 
   -- Setup inline ghost text suggestions (Copilot-style)
   if M.config.suggestion and M.config.suggestion.enabled then
-    local suggestion = require("codetyper.suggestion")
+    local suggestion = require("codetyper.features.completion.suggestion")
     suggestion.setup(M.config.suggestion)
   end
 
   -- Start the event-driven scheduler if enabled
   if M.config.scheduler and M.config.scheduler.enabled then
-    local scheduler = require("codetyper.agent.scheduler")
+    local scheduler = require("codetyper.core.scheduler.scheduler")
     scheduler.start(M.config.scheduler)
   end
 
@@ -80,7 +80,7 @@ function M.setup(opts)
   -- Auto-open Ask panel after a short delay (to let UI settle)
   if M.config.auto_open_ask then
     vim.defer_fn(function()
-      local ask = require("codetyper.ask")
+      local ask = require("codetyper.features.ask.engine")
       if not ask.is_open() then
         ask.open()
       end
diff --git a/lua/codetyper/inject.lua b/lua/codetyper/inject.lua
index 8ced0ed..886c7e6 100644
--- a/lua/codetyper/inject.lua
+++ b/lua/codetyper/inject.lua
@@ -2,14 +2,14 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Inject generated code into target file
 ---@param target_path string Path to target file
 ---@param code string Generated code
 ---@param prompt_type string Type of prompt (refactor, add, document, etc.)
 function M.inject_code(target_path, code, prompt_type)
-  local window = require("codetyper.window")
+  local window = require("codetyper.adapters.nvim.windows")
 
   -- Normalize the target path
   target_path = vim.fn.fnamemodify(target_path, ":p")
@@ -109,7 +109,7 @@ function M.inject_add(bufnr, code)
   local lines = vim.split(code, "\n", { plain = true })
 
   -- Get cursor position in target window
-  local window = require("codetyper.window")
+  local window = require("codetyper.adapters.nvim.windows")
   local target_win = window.get_target_win()
 
   local insert_line
diff --git a/lua/codetyper/parser.lua b/lua/codetyper/parser.lua
index fe5978f..f8aca6a 100644
--- a/lua/codetyper/parser.lua
+++ b/lua/codetyper/parser.lua
@@ -2,7 +2,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Get config with safe fallback
 ---@return table config
diff --git a/lua/codetyper/gitignore.lua b/lua/codetyper/support/gitignore.lua
similarity index 99%
rename from lua/codetyper/gitignore.lua
rename to lua/codetyper/support/gitignore.lua
index 170a144..9105209 100644
--- a/lua/codetyper/gitignore.lua
+++ b/lua/codetyper/support/gitignore.lua
@@ -2,7 +2,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Patterns to add to .gitignore
 local IGNORE_PATTERNS = {
diff --git a/lua/codetyper/health.lua b/lua/codetyper/support/health.lua
similarity index 92%
rename from lua/codetyper/health.lua
rename to lua/codetyper/support/health.lua
index 45dafd3..34cd4b0 100644
--- a/lua/codetyper/health.lua
+++ b/lua/codetyper/support/health.lua
@@ -41,7 +41,7 @@ function M.check()
       health.info("Ollama model: " .. config.llm.ollama.model)
 
       -- Try to check Ollama connectivity
-      local ollama = require("codetyper.llm.ollama")
+      local ollama = require("codetyper.core.llm.ollama")
       ollama.health_check(function(is_ok, err)
         if is_ok then
           vim.schedule(function()
@@ -64,8 +64,8 @@ function M.check()
   end
 
   -- Check .gitignore configuration
-  local utils = require("codetyper.utils")
-  local gitignore = require("codetyper.gitignore")
+  local utils = require("codetyper.support.utils")
+  local gitignore = require("codetyper.support.gitignore")
 
   local root = utils.get_project_root()
   if root then
diff --git a/lua/codetyper/utils/langmap.lua b/lua/codetyper/support/langmap.lua
similarity index 100%
rename from lua/codetyper/utils/langmap.lua
rename to lua/codetyper/support/langmap.lua
diff --git a/lua/codetyper/tree.lua b/lua/codetyper/support/tree.lua
similarity index 99%
rename from lua/codetyper/tree.lua
rename to lua/codetyper/support/tree.lua
index d2e08fe..4ad38d5 100644
--- a/lua/codetyper/tree.lua
+++ b/lua/codetyper/support/tree.lua
@@ -2,7 +2,7 @@
 
 local M = {}
 
-local utils = require("codetyper.utils")
+local utils = require("codetyper.support.utils")
 
 --- Name of the coder folder
 local CODER_FOLDER = ".coder"
diff --git a/lua/codetyper/utils.lua b/lua/codetyper/support/utils.lua
similarity index 100%
rename from lua/codetyper/utils.lua
rename to lua/codetyper/support/utils.lua