migrating autocmds

lua/codetyper/adapters/nvim/autocmds/auto_index_file.lua

@@ -0,0 +1,252 @@
+local utils = require("codetyper.support.utils")
+local autocmds_state = require("codetyper.adapters.nvim.autocmds.state")
+local is_supported_extension = require("codetyper.adapters.nvim.autocmds.is_supported_extension")
+local should_ignore_for_coder = require("codetyper.adapters.nvim.autocmds.should_ignore_for_coder")
+
+--- Auto-index a file by creating/opening its coder companion
+---@param bufnr number Buffer number
+local function auto_index_file(bufnr)
+  if not vim.api.nvim_buf_is_valid(bufnr) then
+    return
+  end
+
+  if autocmds_state.auto_indexed_buffers[bufnr] then
+    return
+  end
+
+  local filepath = vim.api.nvim_buf_get_name(bufnr)
+  if not filepath or filepath == "" then
+    return
+  end
+
+  if utils.is_coder_file(filepath) then
+    return
+  end
+
+  local buftype = vim.bo[bufnr].buftype
+  if buftype ~= "" then
+    return
+  end
+
+  local ext = vim.fn.fnamemodify(filepath, ":e")
+  if ext == "" or not is_supported_extension(ext) then
+    return
+  end
+
+  if should_ignore_for_coder(filepath) then
+    return
+  end
+
+  local codetyper = require("codetyper")
+  local config = codetyper.get_config()
+  if config and config.auto_index == false then
+    return
+  end
+
+  autocmds_state.auto_indexed_buffers[bufnr] = true
+
+  local coder_path = utils.get_coder_path(filepath)
+
+  local coder_exists = utils.file_exists(coder_path)
+
+  if not coder_exists then
+    local filename = vim.fn.fnamemodify(filepath, ":t")
+    local file_ext = vim.fn.fnamemodify(filepath, ":e")
+
+    local comment_prefix = "--"
+    local comment_block_start = "--[["
+    local comment_block_end = "]]"
+    if
+      file_ext == "ts"
+      or file_ext == "tsx"
+      or file_ext == "js"
+      or file_ext == "jsx"
+      or file_ext == "java"
+      or file_ext == "c"
+      or file_ext == "cpp"
+      or file_ext == "cs"
+      or file_ext == "go"
+      or file_ext == "rs"
+    then
+      comment_prefix = "//"
+      comment_block_start = "/*"
+      comment_block_end = "*/"
+    elseif file_ext == "py" or file_ext == "rb" or file_ext == "yaml" or file_ext == "yml" then
+      comment_prefix = "#"
+      comment_block_start = '"""'
+      comment_block_end = '"""'
+    end
+
+    local content = ""
+    pcall(function()
+      local lines = vim.fn.readfile(filepath)
+      if lines then
+        content = table.concat(lines, "\n")
+      end
+    end)
+
+    local functions = extract_functions(content, file_ext)
+    local classes = extract_classes(content, file_ext)
+    local imports = extract_imports(content, file_ext)
+
+    local pseudo_code = {}
+
+    table.insert(
+      pseudo_code,
+      comment_prefix
+        .. " ═══════════════════════════════════════════════════════════"
+    )
+    table.insert(pseudo_code, comment_prefix .. " CODER COMPANION: " .. filename)
+    table.insert(
+      pseudo_code,
+      comment_prefix
+        .. " ═══════════════════════════════════════════════════════════"
+    )
+    table.insert(pseudo_code, comment_prefix .. " This file describes the business logic and behavior of " .. filename)
+    table.insert(pseudo_code, comment_prefix .. " Edit this pseudo-code to guide code generation.")
+    table.insert(pseudo_code, comment_prefix .. "")
+
+    table.insert(
+      pseudo_code,
+      comment_prefix
+        .. " ─────────────────────────────────────────────────────────────"
+    )
+    table.insert(pseudo_code, comment_prefix .. " MODULE PURPOSE:")
+    table.insert(
+      pseudo_code,
+      comment_prefix
+        .. " ─────────────────────────────────────────────────────────────"
+    )
+    table.insert(pseudo_code, comment_prefix .. " TODO: Describe what this module/file is responsible for")
+    table.insert(pseudo_code, comment_prefix .. ' Example: "Handles user authentication and session management"')
+    table.insert(pseudo_code, comment_prefix .. "")
+
+    if #imports > 0 then
+      table.insert(
+        pseudo_code,
+        comment_prefix
+          .. " ─────────────────────────────────────────────────────────────"
+      )
+      table.insert(pseudo_code, comment_prefix .. " DEPENDENCIES:")
+      table.insert(
+        pseudo_code,
+        comment_prefix
+          .. " ─────────────────────────────────────────────────────────────"
+      )
+      for _, imp in ipairs(imports) do
+        table.insert(pseudo_code, comment_prefix .. " • " .. imp)
+      end
+      table.insert(pseudo_code, comment_prefix .. "")
+    end
+
+    if #classes > 0 then
+      table.insert(
+        pseudo_code,
+        comment_prefix
+          .. " ─────────────────────────────────────────────────────────────"
+      )
+      table.insert(pseudo_code, comment_prefix .. " CLASSES:")
+      table.insert(
+        pseudo_code,
+        comment_prefix
+          .. " ─────────────────────────────────────────────────────────────"
+      )
+      for _, class in ipairs(classes) do
+        table.insert(pseudo_code, comment_prefix .. "")
+        table.insert(pseudo_code, comment_prefix .. " class " .. class.name .. ":")
+        table.insert(pseudo_code, comment_prefix .. "   PURPOSE: TODO - describe what this class represents")
+        table.insert(pseudo_code, comment_prefix .. "   RESPONSIBILITIES:")
+        table.insert(pseudo_code, comment_prefix .. "     - TODO: list main responsibilities")
+      end
+      table.insert(pseudo_code, comment_prefix .. "")
+    end
+
+    if #functions > 0 then
+      table.insert(
+        pseudo_code,
+        comment_prefix
+          .. " ─────────────────────────────────────────────────────────────"
+      )
+      table.insert(pseudo_code, comment_prefix .. " FUNCTIONS:")
+      table.insert(
+        pseudo_code,
+        comment_prefix
+          .. " ─────────────────────────────────────────────────────────────"
+      )
+      for _, func in ipairs(functions) do
+        table.insert(pseudo_code, comment_prefix .. "")
+        table.insert(pseudo_code, comment_prefix .. " " .. func.name .. "():")
+        table.insert(pseudo_code, comment_prefix .. "   PURPOSE: TODO - what does this function do?")
+        table.insert(pseudo_code, comment_prefix .. "   INPUTS: TODO - describe parameters")
+        table.insert(pseudo_code, comment_prefix .. "   OUTPUTS: TODO - describe return value")
+        table.insert(pseudo_code, comment_prefix .. "   BEHAVIOR:")
+        table.insert(pseudo_code, comment_prefix .. "     - TODO: describe step-by-step logic")
+      end
+      table.insert(pseudo_code, comment_prefix .. "")
+    end
+
+    if #functions == 0 and #classes == 0 then
+      table.insert(
+        pseudo_code,
+        comment_prefix
+          .. " ─────────────────────────────────────────────────────────────"
+      )
+      table.insert(pseudo_code, comment_prefix .. " PLANNED STRUCTURE:")
+      table.insert(
+        pseudo_code,
+        comment_prefix
+          .. " ─────────────────────────────────────────────────────────────"
+      )
+      table.insert(pseudo_code, comment_prefix .. " TODO: Describe what you want to build in this file")
+      table.insert(pseudo_code, comment_prefix .. "")
+      table.insert(pseudo_code, comment_prefix .. " Example pseudo-code:")
+
+      table.insert(pseudo_code, comment_prefix .. " Create a module that:")
+      table.insert(pseudo_code, comment_prefix .. " 1. Exports a main function")
+      table.insert(pseudo_code, comment_prefix .. " 2. Handles errors gracefully")
+      table.insert(pseudo_code, comment_prefix .. " 3. Returns structured data")
+      table.insert(pseudo_code, comment_prefix .. "")
+    end
+
+    table.insert(
+      pseudo_code,
+      comment_prefix
+        .. " ─────────────────────────────────────────────────────────────"
+    )
+    table.insert(pseudo_code, comment_prefix .. " BUSINESS RULES:")
+    table.insert(
+      pseudo_code,
+      comment_prefix
+        .. " ─────────────────────────────────────────────────────────────"
+    )
+    table.insert(pseudo_code, comment_prefix .. " TODO: Document any business rules, constraints, or requirements")
+    table.insert(pseudo_code, comment_prefix .. " Example:")
+    table.insert(pseudo_code, comment_prefix .. "   - Users must be authenticated before accessing this feature")
+    table.insert(pseudo_code, comment_prefix .. "   - Data must be validated before saving")
+    table.insert(pseudo_code, comment_prefix .. "   - Errors should be logged but not exposed to users")
+    table.insert(pseudo_code, comment_prefix .. "")
+
+    table.insert(
+      pseudo_code,
+      comment_prefix
+        .. " ═══════════════════════════════════════════════════════════"
+    )
+    table.insert(
+      pseudo_code,
+      comment_prefix
+        .. " ═══════════════════════════════════════════════════════════"
+    )
+    table.insert(pseudo_code, "")
+
+    utils.write_file(coder_path, table.concat(pseudo_code, "\n"))
+  end
+
+  local coder_filename = vim.fn.fnamemodify(coder_path, ":t")
+  if coder_exists then
+    utils.notify("Coder companion available: " .. coder_filename, vim.log.levels.DEBUG)
+  else
+    utils.notify("Created coder companion: " .. coder_filename, vim.log.levels.INFO)
+  end
+end
+
+return auto_index_file

lua/codetyper/adapters/nvim/autocmds/check_all_prompts.lua

@@ -0,0 +1,32 @@
+local process_single_prompt = require("codetyper.adapters.nvim.autocmds.process_single_prompt")
+
+--- Check and process all closed prompts in the buffer
+local function check_all_prompts()
+  local find_prompts_in_buffer = require("codetyper.parser.find_prompts_in_buffer")
+  local bufnr = vim.api.nvim_get_current_buf()
+  local current_file = vim.fn.expand("%:p")
+
+  if current_file == "" then
+    return
+  end
+
+  local prompts = find_prompts_in_buffer(bufnr)
+
+  if #prompts == 0 then
+    return
+  end
+
+  local codetyper = require("codetyper")
+  local ct_config = codetyper.get_config()
+  local scheduler_enabled = ct_config and ct_config.scheduler and ct_config.scheduler.enabled
+
+  if not scheduler_enabled then
+    return
+  end
+
+  for _, prompt in ipairs(prompts) do
+    process_single_prompt(bufnr, prompt, current_file)
+  end
+end
+
+return check_all_prompts

lua/codetyper/adapters/nvim/autocmds/check_all_prompts_with_preference.lua

@@ -0,0 +1,35 @@
+local processed_prompts = require("codetyper.constants.constants").processed_prompts
+local get_prompt_key = require("codetyper.adapters.nvim.autocmds.get_prompt_key")
+local check_all_prompts = require("codetyper.adapters.nvim.autocmds.check_all_prompts")
+
+--- Check all prompts with preference check
+--- Only processes if there are unprocessed prompts and auto_process is enabled
+local function check_all_prompts_with_preference()
+  local preferences = require("codetyper.config.preferences")
+  local find_prompts_in_buffer = require("codetyper.parser.find_prompts_in_buffer")
+
+  local bufnr = vim.api.nvim_get_current_buf()
+  local prompts = find_prompts_in_buffer(bufnr)
+  if #prompts == 0 then
+    return
+  end
+
+  local has_unprocessed = false
+  for _, prompt in ipairs(prompts) do
+    local prompt_key = get_prompt_key(bufnr, prompt)
+    if not processed_prompts[prompt_key] then
+      has_unprocessed = true
+      break
+    end
+  end
+
+  if not has_unprocessed then
+    return
+  end
+
+  if auto_process then
+    check_all_prompts()
+  end
+end
+
+return check_all_prompts_with_preference

lua/codetyper/adapters/nvim/autocmds/check_for_closed_prompt.lua

@@ -0,0 +1,187 @@
+local utils = require("codetyper.support.utils")
+local processed_prompts = require("codetyper.constants.constants").processed_prompts
+local is_processing = require("codetyper.constants.constants").is_processing
+local get_prompt_key = require("codetyper.adapters.nvim.autocmds.get_prompt_key")
+local read_attached_files = require("codetyper.adapters.nvim.autocmds.read_attached_files")
+local create_injection_marks = require("codetyper.adapters.nvim.autocmds.create_injection_marks")
+
+--- Check if the buffer has a newly closed prompt and auto-process
+function check_for_closed_prompt()
+  if is_processing then
+    return
+  end
+  is_processing = true
+
+  local has_closing_tag = require("codetyper.parser.has_closing_tag")
+  local get_last_prompt = require("codetyper.parser.get_last_prompt")
+  local clean_prompt = require("codetyper.parser.clean_prompt")
+  local strip_file_references = require("codetyper.parser.strip_file_references")
+
+  local bufnr = vim.api.nvim_get_current_buf()
+  local current_file = vim.fn.expand("%:p")
+
+  if current_file == "" then
+    is_processing = false
+    return
+  end
+
+  local cursor = vim.api.nvim_win_get_cursor(0)
+  local line = cursor[1]
+  local lines = vim.api.nvim_buf_get_lines(bufnr, line - 1, line, false)
+
+  if #lines == 0 then
+    is_processing = false
+    return
+  end
+
+  local current_line = lines[1]
+
+  if has_closing_tag(current_line, config.patterns.close_tag) then
+    local prompt = get_last_prompt(bufnr)
+    if prompt and prompt.content and prompt.content ~= "" then
+      local prompt_key = get_prompt_key(bufnr, prompt)
+
+      if processed_prompts[prompt_key] then
+        is_processing = false
+        return
+      end
+
+      processed_prompts[prompt_key] = true
+
+      local codetyper = require("codetyper")
+      local ct_config = codetyper.get_config()
+      local scheduler_enabled = ct_config and ct_config.scheduler and ct_config.scheduler.enabled
+
+      if scheduler_enabled then
+        vim.schedule(function()
+          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 snapshot = patch_mod.snapshot_buffer(bufnr, {
+            start_line = prompt.start_line,
+            end_line = prompt.end_line,
+          })
+
+          local target_path
+          if utils.is_coder_file(current_file) then
+            target_path = utils.get_target_path(current_file)
+          else
+            target_path = current_file
+          end
+
+          local attached_files = read_attached_files(prompt.content, current_file)
+
+          local cleaned = clean_prompt(strip_file_references(prompt.content))
+
+          local is_from_coder_file = utils.is_coder_file(current_file)
+
+          local target_bufnr = vim.fn.bufnr(target_path)
+          local scope = nil
+          local scope_text = nil
+          local scope_range = nil
+
+          if not is_from_coder_file then
+            if target_bufnr == -1 then
+              target_bufnr = bufnr
+            end
+            scope = scope_mod.resolve_scope(target_bufnr, prompt.start_line, 1)
+            if scope and scope.type ~= "file" then
+              scope_text = scope.text
+              scope_range = {
+                start_line = scope.range.start_row,
+                end_line = scope.range.end_row,
+              }
+            end
+          else
+            if target_bufnr == -1 then
+              target_bufnr = vim.fn.bufadd(target_path)
+              if target_bufnr ~= 0 then
+                vim.fn.bufload(target_bufnr)
+              end
+            end
+          end
+
+          local intent = intent_mod.detect(cleaned)
+
+          if not is_from_coder_file and scope and (scope.type == "function" or scope.type == "method") then
+            if intent.type == "add" or intent.action == "insert" or intent.action == "append" then
+              intent = {
+                type = "complete",
+                scope_hint = "function",
+                confidence = intent.confidence,
+                action = "replace",
+                keywords = intent.keywords,
+              }
+            end
+          end
+
+          if is_from_coder_file and (intent.action == "replace" or intent.type == "complete") then
+            intent = {
+              type = intent.type == "complete" and "add" or intent.type,
+              confidence = intent.confidence,
+              action = "append",
+              keywords = intent.keywords,
+            }
+          end
+
+          local priority = 2
+          if intent.type == "fix" or intent.type == "complete" then
+            priority = 1
+          elseif intent.type == "test" or intent.type == "document" then
+            priority = 3
+          end
+
+          local raw_start = (prompt.injection_range and prompt.injection_range.start_line) or prompt.start_line or 1
+          local raw_end = (prompt.injection_range and prompt.injection_range.end_line) or prompt.end_line or 1
+          local target_line_count = vim.api.nvim_buf_line_count(target_bufnr)
+          target_line_count = math.max(1, target_line_count)
+          local range_start = math.max(1, math.min(raw_start, target_line_count))
+          local range_end = math.max(1, math.min(raw_end, target_line_count))
+          if range_end < range_start then
+            range_end = range_start
+          end
+          local event_range = { start_line = range_start, end_line = range_end }
+
+          local range_for_marks = scope_range or event_range
+          local injection_marks = create_injection_marks(target_bufnr, range_for_marks)
+
+          queue.enqueue({
+            id = queue.generate_id(),
+            bufnr = bufnr,
+            range = event_range,
+            timestamp = os.clock(),
+            changedtick = snapshot.changedtick,
+            content_hash = snapshot.content_hash,
+            prompt_content = cleaned,
+            target_path = target_path,
+            priority = priority,
+            status = "pending",
+            attempt_count = 0,
+            intent = intent,
+            scope = scope,
+            scope_text = scope_text,
+            scope_range = scope_range,
+            attached_files = attached_files,
+            injection_marks = injection_marks,
+          })
+
+          local scope_info = scope
+              and scope.type ~= "file"
+              and string.format(" [%s: %s]", scope.type, scope.name or "anonymous")
+            or ""
+          utils.notify(string.format("Prompt queued: %s%s", intent.type, scope_info), vim.log.levels.INFO)
+        end)
+      else
+        utils.notify("Processing prompt...", vim.log.levels.INFO)
+        vim.schedule(function()
+          vim.cmd("CoderProcess")
+        end)
+      end
+    end
+  end
+  is_processing = false
+end
+
+return check_for_closed_prompt

lua/codetyper/adapters/nvim/autocmds/check_for_closed_prompt_with_preference.lua

@@ -0,0 +1,19 @@
+local check_for_closed_prompt = require("codetyper.adapters.nvim.autocmds.check_for_closed_prompt")
+
+--- Check for closed prompt with preference check
+--- If auto_process is enabled, process; otherwise do nothing (manual mode)
+local function check_for_closed_prompt_with_preference()
+  local find_prompts_in_buffer = require("codetyper.parser.find_prompts_in_buffer")
+
+  local bufnr = vim.api.nvim_get_current_buf()
+  local prompts = find_prompts_in_buffer(bufnr)
+  if #prompts == 0 then
+    return
+  end
+
+  if auto_process then
+    check_for_closed_prompt()
+  end
+end
+
+return check_for_closed_prompt_with_preference

lua/codetyper/adapters/nvim/autocmds/clear_auto_opened.lua

@@ -0,0 +1,9 @@
+local autocmds_state = require("codetyper.adapters.nvim.autocmds.state")
+
+--- Clear auto-opened tracking for a buffer
+---@param bufnr number Buffer number
+local function clear_auto_opened(bufnr)
+  autocmds_state.auto_opened_buffers[bufnr] = nil
+end
+
+return clear_auto_opened

lua/codetyper/adapters/nvim/autocmds/create_injection_marks.lua

@@ -0,0 +1,31 @@
+--- Create extmarks for injection range so position survives user edits
+---@param target_bufnr number Target buffer (where code will be injected)
+---@param range { start_line: number, end_line: number } Range to mark (1-based)
+---@return table|nil injection_marks { start_mark, end_mark } or nil if buffer invalid
+local function create_injection_marks(target_bufnr, range)
+  if not range or target_bufnr == -1 or not vim.api.nvim_buf_is_valid(target_bufnr) then
+    return nil
+  end
+  local line_count = vim.api.nvim_buf_line_count(target_bufnr)
+  if line_count == 0 then
+    return nil
+  end
+  local start_line = math.max(1, math.min(range.start_line, line_count))
+  local end_line = math.max(1, math.min(range.end_line, line_count))
+  if start_line > end_line then
+    end_line = start_line
+  end
+  local marks = require("codetyper.core.marks")
+  local end_line_content = vim.api.nvim_buf_get_lines(target_bufnr, end_line - 1, end_line, false)
+  local end_col_0 = 0
+  if end_line_content and end_line_content[1] then
+    end_col_0 = #end_line_content[1]
+  end
+  local start_mark, end_mark = marks.mark_range(target_bufnr, start_line, end_line, end_col_0)
+  if not start_mark.id or not end_mark.id then
+    return nil
+  end
+  return { start_mark = start_mark, end_mark = end_mark }
+end
+
+return create_injection_marks

lua/codetyper/adapters/nvim/autocmds/get_prompt_key.lua

@@ -0,0 +1,9 @@
+--- Generate a unique key for a prompt
+---@param bufnr number Buffer number
+---@param prompt table Prompt object
+---@return string Unique key
+local function get_prompt_key(bufnr, prompt)
+  return string.format("%d:%d:%d:%s", bufnr, prompt.start_line, prompt.end_line, prompt.content:sub(1, 50))
+end
+
+return get_prompt_key

lua/codetyper/adapters/nvim/autocmds/ignored_directories.lua

@@ -0,0 +1,25 @@
+local ignored_directories = {
+  ".git",
+  ".codetyper",
+  ".claude",
+  ".vscode",
+  ".idea",
+  "node_modules",
+  "vendor",
+  "dist",
+  "build",
+  "target",
+  "__pycache__",
+  ".cache",
+  ".npm",
+  ".yarn",
+  "coverage",
+  ".next",
+  ".nuxt",
+  ".svelte-kit",
+  "out",
+  "bin",
+  "obj",
+}
+
+return ignored_directories

lua/codetyper/adapters/nvim/autocmds/ignored_files.lua

@@ -0,0 +1,48 @@
+local ignored_files = {
+  ".gitignore",
+  ".gitattributes",
+  ".gitmodules",
+  "package-lock.json",
+  "yarn.lock",
+  "pnpm-lock.yaml",
+  "Cargo.lock",
+  "Gemfile.lock",
+  "poetry.lock",
+  "composer.lock",
+  ".env",
+  ".env.local",
+  ".env.development",
+  ".env.production",
+  ".eslintrc",
+  ".eslintrc.json",
+  ".prettierrc",
+  ".prettierrc.json",
+  ".editorconfig",
+  ".dockerignore",
+  "Dockerfile",
+  "docker-compose.yml",
+  "docker-compose.yaml",
+  ".npmrc",
+  ".yarnrc",
+  ".nvmrc",
+  "tsconfig.json",
+  "jsconfig.json",
+  "babel.config.js",
+  "webpack.config.js",
+  "vite.config.js",
+  "rollup.config.js",
+  "jest.config.js",
+  "vitest.config.js",
+  ".stylelintrc",
+  "tailwind.config.js",
+  "postcss.config.js",
+  "README.md",
+  "CHANGELOG.md",
+  "LICENSE",
+  "LICENSE.md",
+  "CONTRIBUTING.md",
+  "Makefile",
+  "CMakeLists.txt",
+}
+
+return ignored_files

lua/codetyper/adapters/nvim/autocmds/is_in_ignored_directory.lua

@@ -0,0 +1,18 @@
+local ignored_directories = require("codetyper.adapters.nvim.autocmds.ignored_directories")
+
+--- Check if a file path contains an ignored directory
+---@param filepath string Full file path
+---@return boolean
+local function is_in_ignored_directory(filepath)
+  for _, dir in ipairs(ignored_directories) do
+    if filepath:match("/" .. dir .. "/") or filepath:match("/" .. dir .. "$") then
+      return true
+    end
+    if filepath:match("^" .. dir .. "/") then
+      return true
+    end
+  end
+  return false
+end
+
+return is_in_ignored_directory

lua/codetyper/adapters/nvim/autocmds/is_supported_extension.lua

@@ -0,0 +1,15 @@
+local supported_extensions = require("codetyper.adapters.nvim.autocmds.supported_extensions")
+
+--- Check if extension is supported for auto-indexing
+---@param ext string File extension
+---@return boolean
+local function is_supported_extension(ext)
+  for _, supported in ipairs(supported_extensions) do
+    if ext == supported then
+      return true
+    end
+  end
+  return false
+end
+
+return is_supported_extension

lua/codetyper/adapters/nvim/autocmds/process_single_prompt.lua

@@ -0,0 +1,178 @@
+local utils = require("codetyper.support.utils")
+local processed_prompts = require("codetyper.constants.constants").processed_prompts
+local get_prompt_key = require("codetyper.adapters.nvim.autocmds.get_prompt_key")
+local read_attached_files = require("codetyper.adapters.nvim.autocmds.read_attached_files")
+local create_injection_marks = require("codetyper.adapters.nvim.autocmds.create_injection_marks")
+
+--- Process a single prompt through the scheduler
+---@param bufnr number Buffer number
+---@param prompt table Prompt object with start_line, end_line, content
+---@param current_file string Current file path
+---@param skip_processed_check? boolean Skip the processed check (for manual mode)
+local function process_single_prompt(bufnr, prompt, current_file, skip_processed_check)
+  local clean_prompt = require("codetyper.parser.clean_prompt")
+  local strip_file_references = require("codetyper.parser.strip_file_references")
+  local scheduler = require("codetyper.core.scheduler.scheduler")
+
+  if not prompt.content or prompt.content == "" then
+    return
+  end
+
+  if not scheduler.status().running then
+    scheduler.start()
+  end
+
+  local prompt_key = get_prompt_key(bufnr, prompt)
+
+  if not skip_processed_check and processed_prompts[prompt_key] then
+    return
+  end
+
+  processed_prompts[prompt_key] = true
+
+  vim.schedule(function()
+    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 snapshot = patch_mod.snapshot_buffer(bufnr, {
+      start_line = prompt.start_line,
+      end_line = prompt.end_line,
+    })
+
+    local target_path
+    local is_from_coder_file = utils.is_coder_file(current_file)
+    if is_from_coder_file then
+      target_path = utils.get_target_path(current_file)
+    else
+      target_path = current_file
+    end
+
+    local attached_files = read_attached_files(prompt.content, current_file)
+
+    local cleaned = clean_prompt(strip_file_references(prompt.content))
+
+    local target_bufnr = vim.fn.bufnr(target_path)
+    local scope = nil
+    local scope_text = nil
+    local scope_range = nil
+
+    if not is_from_coder_file then
+      if target_bufnr == -1 then
+        target_bufnr = bufnr
+      end
+      scope = scope_mod.resolve_scope(target_bufnr, prompt.start_line, 1)
+      if scope and scope.type ~= "file" then
+        scope_text = scope.text
+        scope_range = {
+          start_line = scope.range.start_row,
+          end_line = scope.range.end_row,
+        }
+      end
+    else
+      if target_bufnr == -1 then
+        target_bufnr = vim.fn.bufadd(target_path)
+        if target_bufnr ~= 0 then
+          vim.fn.bufload(target_bufnr)
+        end
+      end
+    end
+
+    local intent = intent_mod.detect(cleaned)
+
+    if prompt.intent_override then
+      intent.action = prompt.intent_override.action or intent.action
+      if prompt.intent_override.type then
+        intent.type = prompt.intent_override.type
+      end
+    elseif not is_from_coder_file and scope and (scope.type == "function" or scope.type == "method") then
+      if intent.type == "add" or intent.action == "insert" or intent.action == "append" then
+        intent = {
+          type = "complete",
+          scope_hint = "function",
+          confidence = intent.confidence,
+          action = "replace",
+          keywords = intent.keywords,
+        }
+      end
+    end
+
+    if is_from_coder_file and (intent.action == "replace" or intent.type == "complete") then
+      intent = {
+        type = intent.type == "complete" and "add" or intent.type,
+        confidence = intent.confidence,
+        action = "append",
+        keywords = intent.keywords,
+      }
+    end
+
+    local project_context = nil
+    if prompt.is_whole_file then
+      pcall(function()
+        local tree = require("codetyper.support.tree")
+        local tree_log = tree.get_tree_log_path()
+        if tree_log and vim.fn.filereadable(tree_log) == 1 then
+          local tree_lines = vim.fn.readfile(tree_log)
+          if tree_lines and #tree_lines > 0 then
+            local tree_content = table.concat(tree_lines, "\n")
+            project_context = tree_content:sub(1, 4000)
+          end
+        end
+      end)
+    end
+
+    local priority = 2
+    if intent.type == "fix" or intent.type == "complete" then
+      priority = 1
+    elseif intent.type == "test" or intent.type == "document" then
+      priority = 3
+    end
+
+    local raw_start = (prompt.injection_range and prompt.injection_range.start_line) or prompt.start_line or 1
+    local raw_end = (prompt.injection_range and prompt.injection_range.end_line) or prompt.end_line or 1
+    local target_line_count = vim.api.nvim_buf_line_count(target_bufnr)
+    target_line_count = math.max(1, target_line_count)
+    local range_start = math.max(1, math.min(raw_start, target_line_count))
+    local range_end = math.max(1, math.min(raw_end, target_line_count))
+    if range_end < range_start then
+      range_end = range_start
+    end
+    local event_range = { start_line = range_start, end_line = range_end }
+
+    local range_for_marks = scope_range or event_range
+    local injection_marks = create_injection_marks(target_bufnr, range_for_marks)
+
+    queue.enqueue({
+      id = queue.generate_id(),
+      bufnr = bufnr,
+      range = event_range,
+      timestamp = os.clock(),
+      changedtick = snapshot.changedtick,
+      content_hash = snapshot.content_hash,
+      prompt_content = cleaned,
+      target_path = target_path,
+      priority = priority,
+      status = "pending",
+      attempt_count = 0,
+      intent = intent,
+      intent_override = prompt.intent_override,
+      scope = scope,
+      scope_text = scope_text,
+      scope_range = scope_range,
+      attached_files = attached_files,
+      injection_marks = injection_marks,
+      injection_range = prompt.injection_range,
+      is_whole_file = prompt.is_whole_file,
+      project_context = project_context,
+    })
+
+    local scope_info = scope
+        and scope.type ~= "file"
+        and string.format(" [%s: %s]", scope.type, scope.name or "anonymous")
+      or ""
+    utils.notify(string.format("Prompt queued: %s%s", intent.type, scope_info), vim.log.levels.INFO)
+  end)
+end
+
+return process_single_prompt

lua/codetyper/adapters/nvim/autocmds/read_attached_files.lua

@@ -0,0 +1,42 @@
+local utils = require("codetyper.support.utils")
+
+--- Read attached files from prompt content
+---@param prompt_content string Prompt content
+---@param base_path string Base path to resolve relative file paths
+---@return table[] attached_files List of {path, content} tables
+local function read_attached_files(prompt_content, base_path)
+  local extract_file_references = require("codetyper.parser.extract_file_references")
+  local file_refs = extract_file_references(prompt_content)
+  local attached = {}
+  local cwd = vim.fn.getcwd()
+  local base_dir = vim.fn.fnamemodify(base_path, ":h")
+
+  for _, ref in ipairs(file_refs) do
+    local file_path = nil
+
+    local cwd_path = cwd .. "/" .. ref
+    if utils.file_exists(cwd_path) then
+      file_path = cwd_path
+    else
+      local rel_path = base_dir .. "/" .. ref
+      if utils.file_exists(rel_path) then
+        file_path = rel_path
+      end
+    end
+
+    if file_path then
+      local content = utils.read_file(file_path)
+      if content then
+        table.insert(attached, {
+          path = ref,
+          full_path = file_path,
+          content = content,
+        })
+      end
+    end
+  end
+
+  return attached
+end
+
+return read_attached_files

lua/codetyper/adapters/nvim/autocmds/reset_processed.lua

@@ -0,0 +1,19 @@
+local utils = require("codetyper.support.utils")
+local processed_prompts = require("codetyper.constants.constants").processed_prompts
+
+--- Reset processed prompts for a buffer (useful for re-processing)
+---@param bufnr? number Buffer number (default: current)
+---@param silent? boolean Suppress notification (default: false)
+local function reset_processed(bufnr, silent)
+  bufnr = bufnr or vim.api.nvim_get_current_buf()
+  for key, _ in pairs(processed_prompts) do
+    if key:match("^" .. bufnr .. ":") then
+      processed_prompts[key] = nil
+    end
+  end
+  if not silent then
+    utils.notify("Prompt history cleared - prompts can be re-processed")
+  end
+end
+
+return reset_processed

lua/codetyper/adapters/nvim/autocmds/schedule_tree_update.lua

@@ -0,0 +1,17 @@
+local tree_update_timer = require("codetyper.constants.constants").tree_update_timer
+local TREE_UPDATE_DEBOUNCE_MS = require("codetyper.constants.constants").TREE_UPDATE_DEBOUNCE_MS
+
+--- Schedule tree update with debounce
+local function schedule_tree_update()
+  if tree_update_timer then
+    tree_update_timer:stop()
+  end
+
+  tree_update_timer = vim.defer_fn(function()
+    local tree = require("codetyper.support.tree")
+    tree.update_tree_log()
+    tree_update_timer = nil
+  end, TREE_UPDATE_DEBOUNCE_MS)
+end
+
+return schedule_tree_update

lua/codetyper/adapters/nvim/autocmds/set_coder_filetype.lua

@@ -0,0 +1,38 @@
+--- Set appropriate filetype for coder files based on extension
+local function set_coder_filetype()
+  local filepath = vim.fn.expand("%:p")
+
+  local ext = filepath:match("%.codetyper%.(%w+)$")
+
+  if ext then
+    local ft_map = {
+      ts = "typescript",
+      tsx = "typescriptreact",
+      js = "javascript",
+      jsx = "javascriptreact",
+      py = "python",
+      lua = "lua",
+      go = "go",
+      rs = "rust",
+      rb = "ruby",
+      java = "java",
+      c = "c",
+      cpp = "cpp",
+      cs = "cs",
+      json = "json",
+      yaml = "yaml",
+      yml = "yaml",
+      md = "markdown",
+      html = "html",
+      css = "css",
+      scss = "scss",
+      vue = "vue",
+      svelte = "svelte",
+    }
+
+    local filetype = ft_map[ext] or ext
+    vim.bo.filetype = filetype
+  end
+end
+
+return set_coder_filetype

lua/codetyper/adapters/nvim/autocmds/setup.lua

@@ -0,0 +1,203 @@
+local utils = require("codetyper.support.utils")
+local AUGROUP = require("codetyper.constants.constants").AUGROUP
+local processed_prompts = require("codetyper.constants.constants").processed_prompts
+local is_processing = require("codetyper.constants.constants").is_processing
+local previous_mode = require("codetyper.constants.constants").previous_mode
+local prompt_process_timer = require("codetyper.constants.constants").prompt_process_timer
+local PROMPT_PROCESS_DEBOUNCE_MS = require("codetyper.constants.constants").PROMPT_PROCESS_DEBOUNCE_MS
+local schedule_tree_update = require("codetyper.adapters.nvim.autocmds.schedule_tree_update")
+local check_for_closed_prompt_with_preference = require("codetyper.adapters.nvim.autocmds.check_for_closed_prompt_with_preference")
+local check_all_prompts_with_preference = require("codetyper.adapters.nvim.autocmds.check_all_prompts_with_preference")
+local set_coder_filetype = require("codetyper.adapters.nvim.autocmds.set_coder_filetype")
+local clear_auto_opened = require("codetyper.adapters.nvim.autocmds.clear_auto_opened")
+local auto_index_file = require("codetyper.adapters.nvim.autocmds.auto_index_file")
+local update_brain_from_file = require("codetyper.adapters.nvim.autocmds.update_brain_from_file")
+
+--- Setup autocommands
+local function setup()
+  local group = vim.api.nvim_create_augroup(AUGROUP, { clear = true })
+
+  vim.api.nvim_create_autocmd("InsertLeave", {
+    group = group,
+    pattern = "*",
+    callback = function()
+      local buftype = vim.bo.buftype
+      if buftype ~= "" then
+        return
+      end
+      local filepath = vim.fn.expand("%:p")
+      if utils.is_coder_file(filepath) and vim.bo.modified then
+        vim.cmd("silent! write")
+      end
+      check_for_closed_prompt_with_preference()
+    end,
+    desc = "Check for closed prompt tags on InsertLeave",
+  })
+
+  vim.api.nvim_create_autocmd("ModeChanged", {
+    group = group,
+    pattern = "*",
+    callback = function(ev)
+      local old_mode = ev.match:match("^(.-):")
+      if old_mode then
+        previous_mode = old_mode
+      end
+    end,
+    desc = "Track previous mode for visual mode detection",
+  })
+
+  vim.api.nvim_create_autocmd("ModeChanged", {
+    group = group,
+    pattern = "*:n",
+    callback = function()
+      local buftype = vim.bo.buftype
+      if buftype ~= "" then
+        return
+      end
+
+      if is_processing then
+        return
+      end
+
+      if previous_mode == "v" or previous_mode == "V" or previous_mode == "\22" then
+        return
+      end
+
+      if prompt_process_timer then
+        prompt_process_timer:stop()
+        prompt_process_timer = nil
+      end
+
+      prompt_process_timer = vim.defer_fn(function()
+        prompt_process_timer = nil
+        local mode = vim.api.nvim_get_mode().mode
+        if mode ~= "n" then
+          return
+        end
+        check_all_prompts_with_preference()
+      end, PROMPT_PROCESS_DEBOUNCE_MS)
+    end,
+    desc = "Auto-process closed prompts when entering normal mode",
+  })
+
+  vim.api.nvim_create_autocmd("CursorHold", {
+    group = group,
+    pattern = "*",
+    callback = function()
+      local buftype = vim.bo.buftype
+      if buftype ~= "" then
+        return
+      end
+      if is_processing then
+        return
+      end
+      local mode = vim.api.nvim_get_mode().mode
+      if mode == "n" then
+        check_all_prompts_with_preference()
+      end
+    end,
+    desc = "Auto-process closed prompts when idle in normal mode",
+  })
+
+  vim.api.nvim_create_autocmd({ "BufRead", "BufNewFile" }, {
+    group = group,
+    pattern = "*.codetyper/*",
+    callback = function()
+      set_coder_filetype()
+    end,
+    desc = "Set filetype for coder files",
+  })
+
+  vim.api.nvim_create_autocmd("BufWipeout", {
+    group = group,
+    pattern = "*.codetyper/*",
+    callback = function(ev)
+      local bufnr = ev.buf
+      for key, _ in pairs(processed_prompts) do
+        if key:match("^" .. bufnr .. ":") then
+          processed_prompts[key] = nil
+        end
+      end
+      clear_auto_opened(bufnr)
+    end,
+    desc = "Cleanup on coder buffer close",
+  })
+
+  vim.api.nvim_create_autocmd({ "BufWritePost", "BufNewFile" }, {
+    group = group,
+    pattern = "*",
+    callback = function(ev)
+      local filepath = ev.file or vim.fn.expand("%:p")
+      if filepath:match("%.codetyper%.") or filepath:match("tree%.log$") then
+        return
+      end
+      if filepath:match("node_modules") or filepath:match("%.git/") or filepath:match("%.codetyper/") then
+        return
+      end
+      schedule_tree_update()
+
+      local indexer_loaded, indexer = pcall(require, "codetyper.indexer")
+      if indexer_loaded then
+        indexer.schedule_index_file(filepath)
+      end
+
+      local brain_loaded, brain = pcall(require, "codetyper.brain")
+      if brain_loaded and brain.is_initialized and brain.is_initialized() then
+        vim.defer_fn(function()
+          update_brain_from_file(filepath)
+        end, 500)
+      end
+    end,
+    desc = "Update tree.log, index, and brain on file creation/save",
+  })
+
+  vim.api.nvim_create_autocmd("BufDelete", {
+    group = group,
+    pattern = "*",
+    callback = function(ev)
+      local filepath = ev.file or ""
+      if filepath == "" or filepath:match("%.codetyper%.") or filepath:match("tree%.log$") then
+        return
+      end
+      schedule_tree_update()
+    end,
+    desc = "Update tree.log on file deletion",
+  })
+
+  vim.api.nvim_create_autocmd("DirChanged", {
+    group = group,
+    pattern = "*",
+    callback = function()
+      schedule_tree_update()
+    end,
+    desc = "Update tree.log on directory change",
+  })
+
+  vim.api.nvim_create_autocmd("VimLeavePre", {
+    group = group,
+    pattern = "*",
+    callback = function()
+      local brain_loaded, brain = pcall(require, "codetyper.brain")
+      if brain_loaded and brain.is_initialized and brain.is_initialized() then
+        brain.shutdown()
+      end
+    end,
+    desc = "Shutdown brain and flush pending changes",
+  })
+
+  vim.api.nvim_create_autocmd("BufEnter", {
+    group = group,
+    pattern = "*",
+    callback = function(ev)
+      vim.defer_fn(function()
+        auto_index_file(ev.buf)
+      end, 100)
+    end,
+    desc = "Auto-index source files with coder companion",
+  })
+
+  local thinking_setup = require("codetyper.adapters.nvim.ui.thinking.setup")
+  thinking_setup()
+end
+
+return setup

lua/codetyper/adapters/nvim/autocmds/should_ignore_for_coder.lua

@@ -0,0 +1,27 @@
+local ignored_files = require("codetyper.adapters.nvim.autocmds.ignored_files")
+local is_in_ignored_directory = require("codetyper.adapters.nvim.autocmds.is_in_ignored_directory")
+
+--- Check if a file should be ignored for coder companion creation
+---@param filepath string Full file path
+---@return boolean
+local function should_ignore_for_coder(filepath)
+  local filename = vim.fn.fnamemodify(filepath, ":t")
+
+  for _, ignored in ipairs(ignored_files) do
+    if filename == ignored then
+      return true
+    end
+  end
+
+  if filename:match("^%.") then
+    return true
+  end
+
+  if is_in_ignored_directory(filepath) then
+    return true
+  end
+
+  return false
+end
+
+return should_ignore_for_coder

lua/codetyper/adapters/nvim/autocmds/state.lua

@@ -0,0 +1,7 @@
+local state = {
+  auto_opened_buffers = {},
+  auto_indexed_buffers = {},
+  brain_update_timers = {},
+}
+
+return state

lua/codetyper/adapters/nvim/autocmds/supported_extensions.lua

@@ -0,0 +1,29 @@
+local supported_extensions = {
+  "ts",
+  "tsx",
+  "js",
+  "jsx",
+  "py",
+  "lua",
+  "go",
+  "rs",
+  "rb",
+  "java",
+  "c",
+  "cpp",
+  "cs",
+  "json",
+  "yaml",
+  "yml",
+  "md",
+  "html",
+  "css",
+  "scss",
+  "vue",
+  "svelte",
+  "php",
+  "sh",
+  "zsh",
+}
+
+return supported_extensions

lua/codetyper/adapters/nvim/autocmds/update_brain_from_file.lua

@@ -0,0 +1,91 @@
+local utils = require("codetyper.support.utils")
+
+--- Update brain with patterns from a file
+---@param filepath string
+local function update_brain_from_file(filepath)
+  local brain_loaded, brain = pcall(require, "codetyper.brain")
+  if not brain_loaded or not brain.is_initialized() then
+    return
+  end
+
+  local content = utils.read_file(filepath)
+  if not content or content == "" then
+    return
+  end
+
+  local ext = vim.fn.fnamemodify(filepath, ":e")
+  local lines = vim.split(content, "\n")
+
+  local functions = {}
+  local classes = {}
+  local imports = {}
+
+  for line_index, line in ipairs(lines) do
+    local func_name = line:match("^%s*function%s+([%w_:%.]+)%s*%(")
+      or line:match("^%s*local%s+function%s+([%w_]+)%s*%(")
+      or line:match("^%s*def%s+([%w_]+)%s*%(")
+      or line:match("^%s*func%s+([%w_]+)%s*%(")
+      or line:match("^%s*async%s+function%s+([%w_]+)%s*%(")
+      or line:match("^%s*public%s+.*%s+([%w_]+)%s*%(")
+      or line:match("^%s*private%s+.*%s+([%w_]+)%s*%(")
+    if func_name then
+      table.insert(functions, { name = func_name, line = line_index })
+    end
+
+    local class_name = line:match("^%s*class%s+([%w_]+)")
+      or line:match("^%s*public%s+class%s+([%w_]+)")
+      or line:match("^%s*interface%s+([%w_]+)")
+      or line:match("^%s*struct%s+([%w_]+)")
+    if class_name then
+      table.insert(classes, { name = class_name, line = line_index })
+    end
+
+    local import_path = line:match("import%s+.*%s+from%s+[\"']([^\"']+)[\"']")
+      or line:match("require%([\"']([^\"']+)[\"']%)")
+      or line:match("from%s+([%w_.]+)%s+import")
+    if import_path then
+      table.insert(imports, import_path)
+    end
+  end
+
+  if #functions == 0 and #classes == 0 then
+    return
+  end
+
+  local parts = {}
+  if #functions > 0 then
+    local func_names = {}
+    for func_index, func_entry in ipairs(functions) do
+      if func_index <= 5 then
+        table.insert(func_names, func_entry.name)
+      end
+    end
+    table.insert(parts, "functions: " .. table.concat(func_names, ", "))
+  end
+  if #classes > 0 then
+    local class_names = {}
+    for _, class_entry in ipairs(classes) do
+      table.insert(class_names, class_entry.name)
+    end
+    table.insert(parts, "classes: " .. table.concat(class_names, ", "))
+  end
+
+  local summary = vim.fn.fnamemodify(filepath, ":t") .. " - " .. table.concat(parts, "; ")
+
+  brain.learn({
+    type = "pattern_detected",
+    file = filepath,
+    timestamp = os.time(),
+    data = {
+      name = summary,
+      description = #functions .. " functions, " .. #classes .. " classes",
+      language = ext,
+      symbols = vim.tbl_map(function(func_entry)
+        return func_entry.name
+      end, functions),
+      example = nil,
+    },
+  })
+end
+
+return update_brain_from_file

lua/codetyper/adapters/nvim/commands.lua

@@ -1,419 +0,0 @@
----@mod codetyper.commands Command definitions for Codetyper.nvim
-
-local M = {}
-
-local transform = require("codetyper.core.transform")
-local utils = require("codetyper.support.utils")
-
---- Refresh tree.log manually
-local function cmd_tree()
-  local tree = require("codetyper.support.tree")
-  if tree.update_tree_log() then
-    utils.notify("Tree log updated: " .. tree.get_tree_log_path())
-  else
-    utils.notify("Failed to update tree log", vim.log.levels.ERROR)
-  end
-end
-
---- Open tree.log file
-local function cmd_tree_view()
-  local tree = require("codetyper.support.tree")
-  local tree_log_path = tree.get_tree_log_path()
-
-  if not tree_log_path then
-    utils.notify("Could not find tree.log", vim.log.levels.WARN)
-    return
-  end
-
-  -- Ensure tree is up to date
-  tree.update_tree_log()
-
-  -- Open in a new split
-  vim.cmd("vsplit " .. vim.fn.fnameescape(tree_log_path))
-  vim.bo.readonly = true
-  vim.bo.modifiable = false
-end
-
---- Reset processed prompts to allow re-processing
-local function cmd_reset()
-  local autocmds = require("codetyper.adapters.nvim.autocmds")
-  autocmds.reset_processed()
-end
-
---- Force update gitignore
-local function cmd_gitignore()
-  local gitignore = require("codetyper.support.gitignore")
-  gitignore.force_update()
-end
-
---- Index the entire project
-local function cmd_index_project()
-  local indexer = require("codetyper.features.indexer")
-
-  utils.notify("Indexing project...", vim.log.levels.INFO)
-
-  indexer.index_project(function(index)
-    if index then
-      local msg = string.format(
-        "Indexed: %d files, %d functions, %d classes, %d exports",
-        index.stats.files,
-        index.stats.functions,
-        index.stats.classes,
-        index.stats.exports
-      )
-      utils.notify(msg, vim.log.levels.INFO)
-    else
-      utils.notify("Failed to index project", vim.log.levels.ERROR)
-    end
-  end)
-end
-
---- Show index status
-local function cmd_index_status()
-  local indexer = require("codetyper.features.indexer")
-  local memory = require("codetyper.features.indexer.memory")
-
-  local status = indexer.get_status()
-  local mem_stats = memory.get_stats()
-
-  local lines = {
-    "Project Index Status",
-    "====================",
-    "",
-  }
-
-  if status.indexed then
-    table.insert(lines, "Status: Indexed")
-    table.insert(lines, "Project Type: " .. (status.project_type or "unknown"))
-    table.insert(lines, "Last Indexed: " .. os.date("%Y-%m-%d %H:%M:%S", status.last_indexed))
-    table.insert(lines, "")
-    table.insert(lines, "Stats:")
-    table.insert(lines, "  Files: " .. (status.stats.files or 0))
-    table.insert(lines, "  Functions: " .. (status.stats.functions or 0))
-    table.insert(lines, "  Classes: " .. (status.stats.classes or 0))
-    table.insert(lines, "  Exports: " .. (status.stats.exports or 0))
-  else
-    table.insert(lines, "Status: Not indexed")
-    table.insert(lines, "Run :CoderIndexProject to index")
-  end
-
-  table.insert(lines, "")
-  table.insert(lines, "Memories:")
-  table.insert(lines, "  Patterns: " .. mem_stats.patterns)
-  table.insert(lines, "  Conventions: " .. mem_stats.conventions)
-  table.insert(lines, "  Symbols: " .. mem_stats.symbols)
-
-  utils.notify(table.concat(lines, "\n"))
-end
-
---- Show learned memories
-local function cmd_memories()
-  local memory = require("codetyper.features.indexer.memory")
-
-  local all = memory.get_all()
-  local lines = {
-    "Learned Memories",
-    "================",
-    "",
-    "Patterns:",
-  }
-
-  local pattern_count = 0
-  for _, mem in pairs(all.patterns) do
-    pattern_count = pattern_count + 1
-    if pattern_count <= 10 then
-      table.insert(lines, "  - " .. (mem.content or ""):sub(1, 60))
-    end
-  end
-  if pattern_count > 10 then
-    table.insert(lines, "  ... and " .. (pattern_count - 10) .. " more")
-  elseif pattern_count == 0 then
-    table.insert(lines, "  (none)")
-  end
-
-  table.insert(lines, "")
-  table.insert(lines, "Conventions:")
-
-  local conv_count = 0
-  for _, mem in pairs(all.conventions) do
-    conv_count = conv_count + 1
-    if conv_count <= 10 then
-      table.insert(lines, "  - " .. (mem.content or ""):sub(1, 60))
-    end
-  end
-  if conv_count > 10 then
-    table.insert(lines, "  ... and " .. (conv_count - 10) .. " more")
-  elseif conv_count == 0 then
-    table.insert(lines, "  (none)")
-  end
-
-  utils.notify(table.concat(lines, "\n"))
-end
-
---- Clear memories
----@param pattern string|nil Optional pattern to match
-local function cmd_forget(pattern)
-  local memory = require("codetyper.features.indexer.memory")
-
-  if not pattern or pattern == "" then
-    -- Confirm before clearing all
-    vim.ui.select({ "Yes", "No" }, {
-      prompt = "Clear all memories?",
-    }, function(choice)
-      if choice == "Yes" then
-        memory.clear()
-        utils.notify("All memories cleared", vim.log.levels.INFO)
-      end
-    end)
-  else
-    memory.clear(pattern)
-    utils.notify("Cleared memories matching: " .. pattern, vim.log.levels.INFO)
-  end
-end
-
---- Main command dispatcher
----@param args table Command arguments
---- Show LLM accuracy statistics
-local function cmd_llm_stats()
-  local llm = require("codetyper.core.llm")
-  local stats = llm.get_accuracy_stats()
-
-  local lines = {
-    "LLM Provider Accuracy Statistics",
-    "================================",
-    "",
-    string.format("Ollama:"),
-    string.format("  Total requests: %d", stats.ollama.total),
-    string.format("  Correct: %d", stats.ollama.correct),
-    string.format("  Accuracy: %.1f%%", stats.ollama.accuracy * 100),
-    "",
-    string.format("Copilot:"),
-    string.format("  Total requests: %d", stats.copilot.total),
-    string.format("  Correct: %d", stats.copilot.correct),
-    string.format("  Accuracy: %.1f%%", stats.copilot.accuracy * 100),
-    "",
-    "Note: Smart selection prefers Ollama when brain memories",
-    "provide enough context. Accuracy improves over time via",
-    "pondering (verification with other LLMs).",
-  }
-
-  vim.notify(table.concat(lines, "\n"), vim.log.levels.INFO)
-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.core.llm")
-  -- Default to ollama for feedback
-  local provider = "ollama"
-
-  llm.report_feedback(provider, was_good)
-  local feedback_type = was_good and "positive" or "negative"
-  utils.notify(string.format("Reported %s feedback for %s", feedback_type, provider), vim.log.levels.INFO)
-end
-
---- Reset LLM accuracy statistics
-local function cmd_llm_reset_stats()
-  local selector = require("codetyper.core.llm.selector")
-  selector.reset_accuracy_stats()
-  utils.notify("LLM accuracy statistics reset", vim.log.levels.INFO)
-end
-
-local function coder_cmd(args)
-  local subcommand = args.fargs[1] or "version"
-
-  local commands = {
-    ["version"] = function()
-      local codetyper = require("codetyper")
-      utils.notify("Codetyper.nvim " .. codetyper.version, vim.log.levels.INFO)
-    end,
-    tree = cmd_tree,
-    ["tree-view"] = cmd_tree_view,
-    reset = cmd_reset,
-    gitignore = cmd_gitignore,
-    ["transform-selection"] = transform.cmd_transform_selection,
-    ["index-project"] = cmd_index_project,
-    ["index-status"] = cmd_index_status,
-    ["llm-stats"] = cmd_llm_stats,
-    ["llm-reset-stats"] = cmd_llm_reset_stats,
-    ["cost"] = function()
-      local cost = require("codetyper.core.cost")
-      cost.toggle()
-    end,
-    ["cost-clear"] = function()
-      local cost = require("codetyper.core.cost")
-      cost.clear()
-    end,
-    ["credentials"] = function()
-      local credentials = require("codetyper.config.credentials")
-      credentials.show_status()
-    end,
-    ["switch-provider"] = function()
-      local credentials = require("codetyper.config.credentials")
-      credentials.interactive_switch_provider()
-    end,
-    ["model"] = function(args)
-      local credentials = require("codetyper.config.credentials")
-      local codetyper = require("codetyper")
-      local config = codetyper.get_config()
-      local provider = config.llm.provider
-
-      if provider ~= "copilot" then
-        utils.notify(
-          "CoderModel is only available when using Copilot provider. Current: " .. provider:upper(),
-          vim.log.levels.WARN
-        )
-        return
-      end
-
-      local model_arg = args.fargs[2]
-      if model_arg and model_arg ~= "" then
-        local cost = credentials.get_copilot_model_cost(model_arg) or "custom"
-        credentials.set_credentials("copilot", { model = model_arg, configured = true })
-        utils.notify("Copilot model set to: " .. model_arg .. " — " .. cost, vim.log.levels.INFO)
-      else
-        credentials.interactive_copilot_config(true)
-      end
-    end,
-  }
-
-  local cmd_fn = commands[subcommand]
-  if cmd_fn then
-    cmd_fn(args)
-  else
-    utils.notify("Unknown subcommand: " .. subcommand, vim.log.levels.ERROR)
-  end
-end
-
---- Setup all commands
-function M.setup()
-  vim.api.nvim_create_user_command("Coder", coder_cmd, {
-    nargs = "?",
-    complete = function()
-      return {
-        "version",
-        "tree",
-        "tree-view",
-        "reset",
-        "gitignore",
-        "transform-selection",
-        "index-project",
-        "index-status",
-        "llm-stats",
-        "llm-reset-stats",
-        "cost",
-        "cost-clear",
-        "credentials",
-        "switch-provider",
-        "model",
-      }
-    end,
-    desc = "Codetyper.nvim commands",
-  })
-
-  vim.api.nvim_create_user_command("CoderTree", function()
-    cmd_tree()
-  end, { desc = "Refresh tree.log" })
-
-  vim.api.nvim_create_user_command("CoderTreeView", function()
-    cmd_tree_view()
-  end, { desc = "View tree.log" })
-
-  vim.api.nvim_create_user_command("CoderTransformSelection", function()
-    transform.cmd_transform_selection()
-  end, { desc = "Transform visual selection with custom prompt input" })
-
-  -- Project indexer commands
-  vim.api.nvim_create_user_command("CoderIndexProject", function()
-    cmd_index_project()
-  end, { desc = "Index the entire project" })
-
-  vim.api.nvim_create_user_command("CoderIndexStatus", function()
-    cmd_index_status()
-  end, { desc = "Show project index status" })
-
-  -- TODO: re-enable CoderMemories, CoderForget when memory UI is reworked
-  -- TODO: re-enable CoderFeedback when feedback loop is reworked
-  -- TODO: re-enable CoderBrain when brain management UI is reworked
-
-  -- Cost estimation command
-  vim.api.nvim_create_user_command("CoderCost", function()
-    local cost = require("codetyper.core.cost")
-    cost.toggle()
-  end, { desc = "Show LLM cost estimation window" })
-
-  -- TODO: re-enable CoderAddApiKey when multi-provider support returns
-
-  vim.api.nvim_create_user_command("CoderCredentials", function()
-    local credentials = require("codetyper.config.credentials")
-    credentials.show_status()
-  end, { desc = "Show credentials status" })
-
-  vim.api.nvim_create_user_command("CoderSwitchProvider", function()
-    local credentials = require("codetyper.config.credentials")
-    credentials.interactive_switch_provider()
-  end, { desc = "Switch active LLM provider" })
-
-  -- Quick model switcher command (Copilot only)
-  vim.api.nvim_create_user_command("CoderModel", function(opts)
-    local credentials = require("codetyper.config.credentials")
-    local codetyper = require("codetyper")
-    local config = codetyper.get_config()
-    local provider = config.llm.provider
-
-    -- Only available for Copilot provider
-    if provider ~= "copilot" then
-      utils.notify(
-        "CoderModel is only available when using Copilot provider. Current: " .. provider:upper(),
-        vim.log.levels.WARN
-      )
-      return
-    end
-
-    -- If an argument is provided, set the model directly
-    if opts.args and opts.args ~= "" then
-      local cost = credentials.get_copilot_model_cost(opts.args) or "custom"
-      credentials.set_credentials("copilot", { model = opts.args, configured = true })
-      utils.notify("Copilot model set to: " .. opts.args .. " — " .. cost, vim.log.levels.INFO)
-      return
-    end
-
-    -- Show interactive selector with costs (silent mode - no OAuth message)
-    credentials.interactive_copilot_config(true)
-  end, {
-    nargs = "?",
-    desc = "Quick switch Copilot model (only available with Copilot provider)",
-    complete = function()
-      local codetyper = require("codetyper")
-      local credentials = require("codetyper.config.credentials")
-      local config = codetyper.get_config()
-      if config.llm.provider == "copilot" then
-        return credentials.get_copilot_model_names()
-      end
-      return {}
-    end,
-  })
-
-  -- Setup default keymaps
-  M.setup_keymaps()
-end
-
---- Setup default keymaps for transform commands
-function M.setup_keymaps()
-  -- Visual mode: transform selection with custom prompt input
-  vim.keymap.set("v", "<leader>ctt", function()
-    transform.cmd_transform_selection()
-  end, {
-    silent = true,
-    desc = "Coder: Transform selection with prompt",
-  })
-  -- Normal mode: prompt only (no selection); request is entered in the prompt
-  vim.keymap.set("n", "<leader>ctt", function()
-    transform.cmd_transform_selection()
-  end, {
-    silent = true,
-    desc = "Coder: Open prompt window",
-  })
-end
-
-return M

lua/codetyper/adapters/nvim/commands/cmd_forget.lua

@@ -0,0 +1,23 @@
+local utils = require("codetyper.support.utils")
+
+--- Clear memories
+---@param pattern string|nil Optional pattern to match
+local function cmd_forget(pattern)
+  local memory = require("codetyper.features.indexer.memory")
+
+  if not pattern or pattern == "" then
+    vim.ui.select({ "Yes", "No" }, {
+      prompt = "Clear all memories?",
+    }, function(choice)
+      if choice == "Yes" then
+        memory.clear()
+        utils.notify("All memories cleared", vim.log.levels.INFO)
+      end
+    end)
+  else
+    memory.clear(pattern)
+    utils.notify("Cleared memories matching: " .. pattern, vim.log.levels.INFO)
+  end
+end
+
+return cmd_forget

lua/codetyper/adapters/nvim/commands/cmd_gitignore.lua

@@ -0,0 +1,7 @@
+--- Force update gitignore
+local function cmd_gitignore()
+  local gitignore = require("codetyper.support.gitignore")
+  gitignore.force_update()
+end
+
+return cmd_gitignore

lua/codetyper/adapters/nvim/commands/cmd_index_project.lua

@@ -0,0 +1,25 @@
+local utils = require("codetyper.support.utils")
+
+--- Index the entire project
+local function cmd_index_project()
+  local indexer = require("codetyper.features.indexer")
+
+  utils.notify("Indexing project...", vim.log.levels.INFO)
+
+  indexer.index_project(function(index)
+    if index then
+      local msg = string.format(
+        "Indexed: %d files, %d functions, %d classes, %d exports",
+        index.stats.files,
+        index.stats.functions,
+        index.stats.classes,
+        index.stats.exports
+      )
+      utils.notify(msg, vim.log.levels.INFO)
+    else
+      utils.notify("Failed to index project", vim.log.levels.ERROR)
+    end
+  end)
+end
+
+return cmd_index_project

lua/codetyper/adapters/nvim/commands/cmd_index_status.lua

@@ -0,0 +1,41 @@
+local utils = require("codetyper.support.utils")
+
+--- Show index status
+local function cmd_index_status()
+  local indexer = require("codetyper.features.indexer")
+  local memory = require("codetyper.features.indexer.memory")
+
+  local status = indexer.get_status()
+  local mem_stats = memory.get_stats()
+
+  local lines = {
+    "Project Index Status",
+    "====================",
+    "",
+  }
+
+  if status.indexed then
+    table.insert(lines, "Status: Indexed")
+    table.insert(lines, "Project Type: " .. (status.project_type or "unknown"))
+    table.insert(lines, "Last Indexed: " .. os.date("%Y-%m-%d %H:%M:%S", status.last_indexed))
+    table.insert(lines, "")
+    table.insert(lines, "Stats:")
+    table.insert(lines, "  Files: " .. (status.stats.files or 0))
+    table.insert(lines, "  Functions: " .. (status.stats.functions or 0))
+    table.insert(lines, "  Classes: " .. (status.stats.classes or 0))
+    table.insert(lines, "  Exports: " .. (status.stats.exports or 0))
+  else
+    table.insert(lines, "Status: Not indexed")
+    table.insert(lines, "Run :CoderIndexProject to index")
+  end
+
+  table.insert(lines, "")
+  table.insert(lines, "Memories:")
+  table.insert(lines, "  Patterns: " .. mem_stats.patterns)
+  table.insert(lines, "  Conventions: " .. mem_stats.conventions)
+  table.insert(lines, "  Symbols: " .. mem_stats.symbols)
+
+  utils.notify(table.concat(lines, "\n"))
+end
+
+return cmd_index_status

lua/codetyper/adapters/nvim/commands/cmd_llm_feedback.lua

@@ -0,0 +1,14 @@
+local utils = require("codetyper.support.utils")
+
+--- 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.core.llm")
+  local provider = "ollama"
+
+  llm.report_feedback(provider, was_good)
+  local feedback_type = was_good and "positive" or "negative"
+  utils.notify(string.format("Reported %s feedback for %s", feedback_type, provider), vim.log.levels.INFO)
+end
+
+return cmd_llm_feedback

lua/codetyper/adapters/nvim/commands/cmd_llm_reset_stats.lua

@@ -0,0 +1,10 @@
+local utils = require("codetyper.support.utils")
+
+--- Reset LLM accuracy statistics
+local function cmd_llm_reset_stats()
+  local selector = require("codetyper.core.llm.selector")
+  selector.reset_accuracy_stats()
+  utils.notify("LLM accuracy statistics reset", vim.log.levels.INFO)
+end
+
+return cmd_llm_reset_stats

lua/codetyper/adapters/nvim/commands/cmd_llm_stats.lua

@@ -0,0 +1,28 @@
+--- Show LLM accuracy statistics
+local function cmd_llm_stats()
+  local llm = require("codetyper.core.llm")
+  local stats = llm.get_accuracy_stats()
+
+  local lines = {
+    "LLM Provider Accuracy Statistics",
+    "================================",
+    "",
+    string.format("Ollama:"),
+    string.format("  Total requests: %d", stats.ollama.total),
+    string.format("  Correct: %d", stats.ollama.correct),
+    string.format("  Accuracy: %.1f%%", stats.ollama.accuracy * 100),
+    "",
+    string.format("Copilot:"),
+    string.format("  Total requests: %d", stats.copilot.total),
+    string.format("  Correct: %d", stats.copilot.correct),
+    string.format("  Accuracy: %.1f%%", stats.copilot.accuracy * 100),
+    "",
+    "Note: Smart selection prefers Ollama when brain memories",
+    "provide enough context. Accuracy improves over time via",
+    "pondering (verification with other LLMs).",
+  }
+
+  vim.notify(table.concat(lines, "\n"), vim.log.levels.INFO)
+end
+
+return cmd_llm_stats

lua/codetyper/adapters/nvim/commands/cmd_memories.lua

@@ -0,0 +1,47 @@
+local utils = require("codetyper.support.utils")
+
+--- Show learned memories
+local function cmd_memories()
+  local memory = require("codetyper.features.indexer.memory")
+
+  local all = memory.get_all()
+  local lines = {
+    "Learned Memories",
+    "================",
+    "",
+    "Patterns:",
+  }
+
+  local pattern_count = 0
+  for _, mem in pairs(all.patterns) do
+    pattern_count = pattern_count + 1
+    if pattern_count <= 10 then
+      table.insert(lines, "  - " .. (mem.content or ""):sub(1, 60))
+    end
+  end
+  if pattern_count > 10 then
+    table.insert(lines, "  ... and " .. (pattern_count - 10) .. " more")
+  elseif pattern_count == 0 then
+    table.insert(lines, "  (none)")
+  end
+
+  table.insert(lines, "")
+  table.insert(lines, "Conventions:")
+
+  local conv_count = 0
+  for _, mem in pairs(all.conventions) do
+    conv_count = conv_count + 1
+    if conv_count <= 10 then
+      table.insert(lines, "  - " .. (mem.content or ""):sub(1, 60))
+    end
+  end
+  if conv_count > 10 then
+    table.insert(lines, "  ... and " .. (conv_count - 10) .. " more")
+  elseif conv_count == 0 then
+    table.insert(lines, "  (none)")
+  end
+
+  utils.notify(table.concat(lines, "\n"))
+end
+
+return cmd_memories

lua/codetyper/adapters/nvim/commands/cmd_reset.lua

@@ -0,0 +1,7 @@
+--- Reset processed prompts to allow re-processing
+local function cmd_reset()
+  local reset_processed = require("codetyper.adapters.nvim.autocmds.reset_processed")
+  reset_processed()
+end
+
+return cmd_reset

lua/codetyper/adapters/nvim/commands/cmd_tree.lua

@@ -0,0 +1,13 @@
+local utils = require("codetyper.support.utils")
+
+--- Refresh tree.log manually
+local function cmd_tree()
+  local tree = require("codetyper.support.tree")
+  if tree.update_tree_log() then
+    utils.notify("Tree log updated: " .. tree.get_tree_log_path())
+  else
+    utils.notify("Failed to update tree log", vim.log.levels.ERROR)
+  end
+end
+
+return cmd_tree

lua/codetyper/adapters/nvim/commands/cmd_tree_view.lua

@@ -0,0 +1,20 @@
+local utils = require("codetyper.support.utils")
+
+--- Open tree.log file in a vertical split
+local function cmd_tree_view()
+  local tree = require("codetyper.support.tree")
+  local tree_log_path = tree.get_tree_log_path()
+
+  if not tree_log_path then
+    utils.notify("Could not find tree.log", vim.log.levels.WARN)
+    return
+  end
+
+  tree.update_tree_log()
+
+  vim.cmd("vsplit " .. vim.fn.fnameescape(tree_log_path))
+  vim.bo.readonly = true
+  vim.bo.modifiable = false
+end
+
+return cmd_tree_view

lua/codetyper/adapters/nvim/commands/coder_cmd.lua

@@ -0,0 +1,80 @@
+local utils = require("codetyper.support.utils")
+local transform = require("codetyper.core.transform")
+local cmd_tree = require("codetyper.adapters.nvim.commands.cmd_tree")
+local cmd_tree_view = require("codetyper.adapters.nvim.commands.cmd_tree_view")
+local cmd_reset = require("codetyper.adapters.nvim.commands.cmd_reset")
+local cmd_gitignore = require("codetyper.adapters.nvim.commands.cmd_gitignore")
+local cmd_index_project = require("codetyper.adapters.nvim.commands.cmd_index_project")
+local cmd_index_status = require("codetyper.adapters.nvim.commands.cmd_index_status")
+local cmd_llm_stats = require("codetyper.adapters.nvim.commands.cmd_llm_stats")
+local cmd_llm_reset_stats = require("codetyper.adapters.nvim.commands.cmd_llm_reset_stats")
+
+--- Main command dispatcher
+---@param args table Command arguments
+local function coder_cmd(args)
+  local subcommand = args.fargs[1] or "version"
+
+  local commands = {
+    ["version"] = function()
+      local codetyper = require("codetyper")
+      utils.notify("Codetyper.nvim " .. codetyper.version, vim.log.levels.INFO)
+    end,
+    tree = cmd_tree,
+    ["tree-view"] = cmd_tree_view,
+    reset = cmd_reset,
+    gitignore = cmd_gitignore,
+    ["transform-selection"] = transform.cmd_transform_selection,
+    ["index-project"] = cmd_index_project,
+    ["index-status"] = cmd_index_status,
+    ["llm-stats"] = cmd_llm_stats,
+    ["llm-reset-stats"] = cmd_llm_reset_stats,
+    ["cost"] = function()
+      local cost = require("codetyper.core.cost")
+      cost.toggle()
+    end,
+    ["cost-clear"] = function()
+      local cost = require("codetyper.core.cost")
+      cost.clear()
+    end,
+    ["credentials"] = function()
+      local credentials = require("codetyper.config.credentials")
+      credentials.show_status()
+    end,
+    ["switch-provider"] = function()
+      local credentials = require("codetyper.config.credentials")
+      credentials.interactive_switch_provider()
+    end,
+    ["model"] = function(cmd_args)
+      local credentials = require("codetyper.config.credentials")
+      local codetyper = require("codetyper")
+      local config = codetyper.get_config()
+      local provider = config.llm.provider
+
+      if provider ~= "copilot" then
+        utils.notify(
+          "CoderModel is only available when using Copilot provider. Current: " .. provider:upper(),
+          vim.log.levels.WARN
+        )
+        return
+      end
+
+      local model_arg = cmd_args.fargs[2]
+      if model_arg and model_arg ~= "" then
+        local model_cost = credentials.get_copilot_model_cost(model_arg) or "custom"
+        credentials.set_credentials("copilot", { model = model_arg, configured = true })
+        utils.notify("Copilot model set to: " .. model_arg .. " — " .. model_cost, vim.log.levels.INFO)
+      else
+        credentials.interactive_copilot_config(true)
+      end
+    end,
+  }
+
+  local cmd_fn = commands[subcommand]
+  if cmd_fn then
+    cmd_fn(args)
+  else
+    utils.notify("Unknown subcommand: " .. subcommand, vim.log.levels.ERROR)
+  end
+end
+
+return coder_cmd

lua/codetyper/adapters/nvim/commands/setup.lua

@@ -0,0 +1,116 @@
+local utils = require("codetyper.support.utils")
+local transform = require("codetyper.core.transform")
+local coder_cmd = require("codetyper.adapters.nvim.commands.coder_cmd")
+local cmd_tree = require("codetyper.adapters.nvim.commands.cmd_tree")
+local cmd_tree_view = require("codetyper.adapters.nvim.commands.cmd_tree_view")
+local cmd_index_project = require("codetyper.adapters.nvim.commands.cmd_index_project")
+local cmd_index_status = require("codetyper.adapters.nvim.commands.cmd_index_status")
+local setup_keymaps = require("codetyper.adapters.nvim.commands.setup_keymaps")
+
+--- Setup all commands
+local function setup()
+  vim.api.nvim_create_user_command("Coder", coder_cmd, {
+    nargs = "?",
+    complete = function()
+      return {
+        "version",
+        "tree",
+        "tree-view",
+        "reset",
+        "gitignore",
+        "transform-selection",
+        "index-project",
+        "index-status",
+        "llm-stats",
+        "llm-reset-stats",
+        "cost",
+        "cost-clear",
+        "credentials",
+        "switch-provider",
+        "model",
+      }
+    end,
+    desc = "Codetyper.nvim commands",
+  })
+
+  vim.api.nvim_create_user_command("CoderTree", function()
+    cmd_tree()
+  end, { desc = "Refresh tree.log" })
+
+  vim.api.nvim_create_user_command("CoderTreeView", function()
+    cmd_tree_view()
+  end, { desc = "View tree.log" })
+
+  vim.api.nvim_create_user_command("CoderTransformSelection", function()
+    transform.cmd_transform_selection()
+  end, { desc = "Transform visual selection with custom prompt input" })
+
+  vim.api.nvim_create_user_command("CoderIndexProject", function()
+    cmd_index_project()
+  end, { desc = "Index the entire project" })
+
+  vim.api.nvim_create_user_command("CoderIndexStatus", function()
+    cmd_index_status()
+  end, { desc = "Show project index status" })
+
+  -- TODO: re-enable CoderMemories, CoderForget when memory UI is reworked
+  -- TODO: re-enable CoderFeedback when feedback loop is reworked
+  -- TODO: re-enable CoderBrain when brain management UI is reworked
+
+  vim.api.nvim_create_user_command("CoderCost", function()
+    local cost = require("codetyper.core.cost")
+    cost.toggle()
+  end, { desc = "Show LLM cost estimation window" })
+
+  -- TODO: re-enable CoderAddApiKey when multi-provider support returns
+
+  vim.api.nvim_create_user_command("CoderCredentials", function()
+    local credentials = require("codetyper.config.credentials")
+    credentials.show_status()
+  end, { desc = "Show credentials status" })
+
+  vim.api.nvim_create_user_command("CoderSwitchProvider", function()
+    local credentials = require("codetyper.config.credentials")
+    credentials.interactive_switch_provider()
+  end, { desc = "Switch active LLM provider" })
+
+  vim.api.nvim_create_user_command("CoderModel", function(opts)
+    local credentials = require("codetyper.config.credentials")
+    local codetyper = require("codetyper")
+    local config = codetyper.get_config()
+    local provider = config.llm.provider
+
+    if provider ~= "copilot" then
+      utils.notify(
+        "CoderModel is only available when using Copilot provider. Current: " .. provider:upper(),
+        vim.log.levels.WARN
+      )
+      return
+    end
+
+    if opts.args and opts.args ~= "" then
+      local model_cost = credentials.get_copilot_model_cost(opts.args) or "custom"
+      credentials.set_credentials("copilot", { model = opts.args, configured = true })
+      utils.notify("Copilot model set to: " .. opts.args .. " — " .. model_cost, vim.log.levels.INFO)
+      return
+    end
+
+    credentials.interactive_copilot_config(true)
+  end, {
+    nargs = "?",
+    desc = "Quick switch Copilot model (only available with Copilot provider)",
+    complete = function()
+      local codetyper = require("codetyper")
+      local credentials = require("codetyper.config.credentials")
+      local config = codetyper.get_config()
+      if config.llm.provider == "copilot" then
+        return credentials.get_copilot_model_names()
+      end
+      return {}
+    end,
+  })
+
+  setup_keymaps()
+end
+
+return setup

lua/codetyper/adapters/nvim/commands/setup_keymaps.lua

@@ -0,0 +1,19 @@
+local transform = require("codetyper.core.transform")
+
+--- Setup default keymaps for transform commands
+local function setup_keymaps()
+  vim.keymap.set("v", "<leader>ctt", function()
+    transform.cmd_transform_selection()
+  end, {
+    silent = true,
+    desc = "Coder: Transform selection with prompt",
+  })
+  vim.keymap.set("n", "<leader>ctt", function()
+    transform.cmd_transform_selection()
+  end, {
+    silent = true,
+    desc = "Coder: Open prompt window",
+  })
+end
+
+return setup_keymaps

lua/codetyper/core/transform.lua

@@ -334,8 +334,8 @@ function M.cmd_transform_selection()
       intent_override = doc_intent_override,
       is_whole_file = is_whole_file,
     }
-    local autocmds = require("codetyper.adapters.nvim.autocmds")
-    autocmds.process_single_prompt(bufnr, prompt, filepath, true)
+    local process_single_prompt = require("codetyper.adapters.nvim.autocmds.process_single_prompt")
+    process_single_prompt(bufnr, prompt, filepath, true)
   end
 
   local augroup = vim.api.nvim_create_augroup("CodetyperPrompt_" .. prompt_buf, { clear = true })

lua/codetyper/init.lua

@@ -28,17 +28,17 @@ function M.setup(opts)
   M.config = config.setup(opts)
 
   -- Initialize modules
-  local commands = require("codetyper.adapters.nvim.commands")
+  local commands_setup = require("codetyper.adapters.nvim.commands.setup")
   local gitignore = require("codetyper.support.gitignore")
-  local autocmds = require("codetyper.adapters.nvim.autocmds")
+  local autocmds_setup = require("codetyper.adapters.nvim.autocmds.setup")
   local tree = require("codetyper.support.tree")
   local completion = require("codetyper.features.completion.inline")
 
   -- Register commands
-  commands.setup()
+  commands_setup()
 
   -- Setup autocommands
-  autocmds.setup()
+  autocmds_setup()
 
   -- Setup file reference completion
   completion.setup()