From 0a1429a823d921ef3c5c09e5866f51c728c6ed4c Mon Sep 17 00:00:00 2001
From: Carlos Gutierrez <cargdev@gmail.com>
Date: Tue, 17 Feb 2026 00:15:40 -0500
Subject: [PATCH] Adding the functionallity and refactoring

---
 lua/codetyper/adapters/nvim/autocmds.lua   |  18 +-
 lua/codetyper/adapters/nvim/commands.lua   | 616 +--------------------
 lua/codetyper/config/defaults.lua          | 206 +++----
 lua/codetyper/core/diff/patch.lua          |  30 +-
 lua/codetyper/core/scheduler/scheduler.lua |  32 ++
 lua/codetyper/core/transform.lua           | 224 ++++++++
 lua/codetyper/init.lua                     |  78 +--
 tests/spec/config_spec.lua                 |  12 -
 8 files changed, 423 insertions(+), 793 deletions(-)
 create mode 100644 lua/codetyper/core/transform.lua

diff --git a/lua/codetyper/adapters/nvim/autocmds.lua b/lua/codetyper/adapters/nvim/autocmds.lua
index 3a70454..ec6aaea 100644
--- a/lua/codetyper/adapters/nvim/autocmds.lua
+++ b/lua/codetyper/adapters/nvim/autocmds.lua
@@ -322,22 +322,12 @@ local function create_injection_marks(target_bufnr, range)
 		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_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
-	)
+	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
@@ -540,7 +530,9 @@ function M.check_for_closed_prompt()
 					end
 
 					-- Use captured injection range when provided, else prompt.start_line/end_line
-					local raw_start = (prompt.injection_range and prompt.injection_range.start_line) or prompt.start_line or 1
+					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 tc = vim.api.nvim_buf_line_count(target_bufnr)
 					tc = math.max(1, tc)
diff --git a/lua/codetyper/adapters/nvim/commands.lua b/lua/codetyper/adapters/nvim/commands.lua
index 119b33f..f96c855 100644
--- a/lua/codetyper/adapters/nvim/commands.lua
+++ b/lua/codetyper/adapters/nvim/commands.lua
@@ -2,222 +2,8 @@
 
 local M = {}
 
+local transform = require("codetyper.core.transform")
 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
-local function cmd_open(opts)
-	opts = opts or {}
-
-	local current_file = vim.fn.expand("%:p")
-
-	-- If no file is open, prompt user to select one
-	if current_file == "" or vim.bo.buftype ~= "" then
-		-- Use telescope or vim.ui.select to pick a file
-		if pcall(require, "telescope") then
-			require("telescope.builtin").find_files({
-				prompt_title = "Select file for Coder",
-				attach_mappings = function(prompt_bufnr, map)
-					local actions = require("telescope.actions")
-					local action_state = require("telescope.actions.state")
-
-					actions.select_default:replace(function()
-						actions.close(prompt_bufnr)
-						local selection = action_state.get_selected_entry()
-						if selection then
-							local target_path = selection.path or selection[1]
-							local coder_path = utils.get_coder_path(target_path)
-							window.open_split(target_path, coder_path)
-						end
-					end)
-					return true
-				end,
-			})
-		else
-			-- Fallback to input prompt
-			vim.ui.input({ prompt = "Enter file path: " }, function(input)
-				if input and input ~= "" then
-					local target_path = vim.fn.fnamemodify(input, ":p")
-					local coder_path = utils.get_coder_path(target_path)
-					window.open_split(target_path, coder_path)
-				end
-			end)
-		end
-		return
-	end
-
-	local target_path, coder_path
-
-	-- Check if current file is a coder file
-	if utils.is_coder_file(current_file) then
-		coder_path = current_file
-		target_path = utils.get_target_path(current_file)
-	else
-		target_path = current_file
-		coder_path = utils.get_coder_path(current_file)
-	end
-
-	window.open_split(target_path, coder_path)
-end
-
---- Close coder view
-local function cmd_close()
-	window.close_split()
-end
-
---- Toggle coder view
-local function cmd_toggle()
-	local current_file = vim.fn.expand("%:p")
-
-	if current_file == "" then
-		utils.notify("No file in current buffer", vim.log.levels.WARN)
-		return
-	end
-
-	local target_path, coder_path
-
-	if utils.is_coder_file(current_file) then
-		coder_path = current_file
-		target_path = utils.get_target_path(current_file)
-	else
-		target_path = current_file
-		coder_path = utils.get_coder_path(current_file)
-	end
-
-	window.toggle_split(target_path, coder_path)
-end
-
---- Return editor dimensions (from UI, like 99 plugin)
----@return number width
----@return number height
-local function get_ui_dimensions()
-	local ui = vim.api.nvim_list_uis()[1]
-	if ui then
-		return ui.width, ui.height
-	end
-	return vim.o.columns, vim.o.lines
-end
-
---- Centered floating window config for prompt (2/3 width, 1/3 height)
----@return table { width, height, row, col, border }
-local function create_centered_window()
-	local width, height = get_ui_dimensions()
-	local win_width = math.floor(width * 2 / 3)
-	local win_height = math.floor(height / 3)
-	return {
-		width = win_width,
-		height = win_height,
-		row = math.floor((height - win_height) / 2),
-		col = math.floor((width - win_width) / 2),
-		border = "rounded",
-	}
-end
-
---- Build enhanced user prompt with context
----@param clean_prompt string The cleaned user prompt
----@param context table Context information
----@return string Enhanced prompt
-local function build_user_prompt(clean_prompt, context)
-	local enhanced = "TASK: " .. clean_prompt .. "\n\n"
-
-	enhanced = enhanced .. "REQUIREMENTS:\n"
-	enhanced = enhanced .. "- Generate ONLY " .. (context.language or "code") .. " code\n"
-	enhanced = enhanced .. "- NO markdown code blocks (no ```)\n"
-	enhanced = enhanced .. "- NO explanations or comments about what you did\n"
-	enhanced = enhanced .. "- Match the coding style of the existing file exactly\n"
-	enhanced = enhanced .. "- Output must be ready to insert directly into the file\n"
-
-	return enhanced
-end
-
---- Process prompt at cursor and generate code
-local function cmd_process()
-	local parser = require("codetyper.parser")
-	local llm = require("codetyper.core.llm")
-
-	local bufnr = vim.api.nvim_get_current_buf()
-	local current_file = vim.fn.expand("%:p")
-
-	if not utils.is_coder_file(current_file) then
-		utils.notify("Not a coder file. Use *.coder.* files", vim.log.levels.WARN)
-		return
-	end
-
-	local prompt = parser.get_last_prompt(bufnr)
-	if not prompt then
-		utils.notify("No prompt found. Use /@ your prompt @/", vim.log.levels.WARN)
-		return
-	end
-
-	local target_path = utils.get_target_path(current_file)
-	local prompt_type = parser.detect_prompt_type(prompt.content)
-	local context = llm.build_context(target_path, prompt_type)
-	local clean_prompt = parser.clean_prompt(prompt.content)
-
-	-- Build enhanced prompt with explicit instructions
-	local enhanced_prompt = build_user_prompt(clean_prompt, context)
-
-	utils.notify("Processing: " .. clean_prompt:sub(1, 50) .. "...", vim.log.levels.INFO)
-
-	llm.generate(enhanced_prompt, context, function(response, err)
-		if err then
-			utils.notify("Generation failed: " .. err, vim.log.levels.ERROR)
-			return
-		end
-
-		if response then
-			-- Inject code into target file
-			local inject = require("codetyper.inject")
-			inject.inject_code(target_path, response, prompt_type)
-			utils.notify("Code generated and injected!", vim.log.levels.INFO)
-		end
-	end)
-end
-
---- Show plugin status
-local function cmd_status()
-	local codetyper = require("codetyper")
-	local config = codetyper.get_config()
-	local tree = require("codetyper.support.tree")
-
-	local stats = tree.get_stats()
-
-	local status = {
-		"Codetyper.nvim Status",
-		"====================",
-		"",
-		"Provider: " .. config.llm.provider,
-	}
-
-	if config.llm.provider == "ollama" then
-		table.insert(status, "Ollama Host: " .. config.llm.ollama.host)
-		table.insert(status, "Ollama Model: " .. config.llm.ollama.model)
-	elseif config.llm.provider == "openai" then
-		local has_key = (config.llm.openai.api_key or vim.env.OPENAI_API_KEY) ~= nil
-		table.insert(status, "OpenAI API Key: " .. (has_key and "configured" or "NOT SET"))
-		table.insert(status, "OpenAI Model: " .. config.llm.openai.model)
-	elseif config.llm.provider == "gemini" then
-		local has_key = (config.llm.gemini.api_key or vim.env.GEMINI_API_KEY) ~= nil
-		table.insert(status, "Gemini API Key: " .. (has_key and "configured" or "NOT SET"))
-		table.insert(status, "Gemini Model: " .. config.llm.gemini.model)
-	elseif config.llm.provider == "copilot" then
-		table.insert(status, "Copilot Model: " .. config.llm.copilot.model)
-	end
-
-	table.insert(status, "")
-	table.insert(status, "Window Position: " .. config.window.position)
-	table.insert(status, "Window Width: " .. tostring(config.window.width * 100) .. "%")
-	table.insert(status, "")
-	table.insert(status, "View Open: " .. (window.is_open() and "yes" or "no"))
-	table.insert(status, "")
-	table.insert(status, "Project Stats:")
-	table.insert(status, "  Files: " .. stats.files)
-	table.insert(status, "  Directories: " .. stats.directories)
-	table.insert(status, "  Tree Log: " .. (tree.get_tree_log_path() or "N/A"))
-
-	utils.notify(table.concat(status, "\n"))
-end
 
 --- Refresh tree.log manually
 local function cmd_tree()
@@ -260,248 +46,6 @@ local function cmd_gitignore()
 	gitignore.force_update()
 end
 
---- Switch focus between coder and target windows
-local function cmd_focus()
-	if not window.is_open() then
-		utils.notify("Coder view not open", vim.log.levels.WARN)
-		return
-	end
-
-	local current_win = vim.api.nvim_get_current_win()
-	if current_win == window.get_coder_win() then
-		window.focus_target()
-	else
-		window.focus_coder()
-	end
-end
-
---- Transform prompts within a line range (for visual selection)
---- Uses the same processing logic as automatic mode for consistent results
----@param start_line number Start line (1-indexed)
----@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.adapters.nvim.autocmds")
-
-	local bufnr = vim.api.nvim_get_current_buf()
-	local filepath = vim.fn.expand("%:p")
-
-	if filepath == "" then
-		utils.notify("No file in current buffer", vim.log.levels.WARN)
-		return
-	end
-
-	-- Find all prompts in the current buffer
-	local all_prompts = parser.find_prompts_in_buffer(bufnr)
-
-	-- Filter prompts that are within the selected range
-	local prompts = {}
-	for _, prompt in ipairs(all_prompts) do
-		if prompt.start_line >= start_line and prompt.end_line <= end_line then
-			table.insert(prompts, prompt)
-		end
-	end
-
-	if #prompts == 0 then
-		utils.notify(
-			"No /@ @/ tags found in selection (lines " .. start_line .. "-" .. end_line .. ")",
-			vim.log.levels.INFO
-		)
-		return
-	end
-
-	utils.notify("Transforming " .. #prompts .. " prompt(s)...", vim.log.levels.INFO)
-
-	-- Process each prompt using the same logic as automatic mode (skip processed check for manual mode)
-	for _, prompt in ipairs(prompts) do
-		autocmds.process_single_prompt(bufnr, prompt, filepath, true)
-	end
-end
-
---- Get visual selection text
----@return string|nil selected_text The selected text or nil
-local function get_visual_selection()
-	local mode = vim.api.nvim_get_mode().mode
-	-- Third argument must be a Vim dictionary; empty Lua table can be treated as list
-	local opts = vim.empty_dict()
-	-- \22 is an escaped version of <c-v>
-	if mode == "v" or mode == "V" or mode == "\22" then
-		opts = { type = mode }
-	end
-	return vim.fn.getregion(vim.fn.getpos("v"), vim.fn.getpos("."), opts)
-end
-
---- Transform visual selection with custom prompt input
---- Opens input window for prompt, processes selection on confirm.
---- When nothing is selected (e.g. from Normal mode), only the prompt is requested.
-local function cmd_transform_selection()
-	local logger = require("codetyper.support.logger")
-	logger.func_entry("commands", "cmd_transform_selection", {})
-	-- Get visual selection (getregion returns a table of lines); may be empty in Normal mode
-	local selection = get_visual_selection()
-	local selection_text = type(selection) == "table" and table.concat(selection, "\n") or tostring(selection or "")
-	local has_selection = selection_text and #selection_text >= 4
-
-	if has_selection then
-		logger.debug(
-			"commands",
-			"Visual selection: " .. selection_text:sub(1, 100) .. (#selection_text > 100 and "..." or "")
-		)
-		logger.info("commands", "Selected " .. #selection_text .. " characters, opening prompt input...")
-	else
-		logger.info("commands", "No selection, opening prompt input only...")
-	end
-
-	local bufnr = vim.api.nvim_get_current_buf()
-	local filepath = vim.fn.expand("%:p")
-	local line_count = vim.api.nvim_buf_line_count(bufnr)
-	line_count = math.max(1, line_count)
-
-	-- Range for injection: selection, or whole file when no selection
-	local start_line, end_line
-	if has_selection then
-		start_line = vim.fn.line("'<")
-		-- Derive end_line from selection content so range matches selected lines (''>' can be wrong after UI changes)
-		local selection_lines = type(selection) == "table" and #selection or #vim.split(selection_text, "\n", { plain = true })
-		selection_lines = math.max(1, selection_lines)
-		end_line = math.min(start_line + selection_lines - 1, line_count)
-	else
-		-- No selection: apply to whole file so the LLM works on the entire file
-		start_line = 1
-		end_line = line_count
-	end
-	-- Clamp to valid 1-based range (avoid 0 or out-of-bounds)
-	start_line = math.max(1, math.min(start_line, line_count))
-	end_line = math.max(1, math.min(end_line, line_count))
-	if end_line < start_line then
-		end_line = start_line
-	end
-
-	-- Capture injection range so we know exactly where to apply the generated code later
-	local injection_range = { start_line = start_line, end_line = end_line }
-	local range_line_count = end_line - start_line + 1
-	logger.info("commands", string.format("Injection range: lines %d-%d (%d lines) – changes will replace this range", start_line, end_line, range_line_count))
-
-	-- Open centered prompt window (pattern from 99: acwrite + BufWriteCmd to submit, BufLeave to keep focus)
-	local prompt_buf = vim.api.nvim_create_buf(false, true)
-	vim.bo[prompt_buf].buftype = "acwrite"
-	vim.bo[prompt_buf].bufhidden = "wipe"
-	vim.bo[prompt_buf].filetype = "markdown"
-	vim.bo[prompt_buf].swapfile = false
-	vim.api.nvim_buf_set_name(prompt_buf, "codetyper-prompt")
-
-	local win_opts = create_centered_window()
-	local prompt_win = vim.api.nvim_open_win(prompt_buf, true, {
-		relative = "editor",
-		row = win_opts.row,
-		col = win_opts.col,
-		width = win_opts.width,
-		height = win_opts.height,
-		style = "minimal",
-		border = win_opts.border,
-		title = has_selection and " Enter prompt for selection " or " Enter prompt ",
-		title_pos = "center",
-	})
-	vim.wo[prompt_win].wrap = true
-	vim.api.nvim_set_current_win(prompt_win)
-
-	local function close_prompt()
-		if prompt_win and vim.api.nvim_win_is_valid(prompt_win) then
-			vim.api.nvim_win_close(prompt_win, true)
-		end
-		if prompt_buf and vim.api.nvim_buf_is_valid(prompt_buf) then
-			vim.api.nvim_buf_delete(prompt_buf, { force = true })
-		end
-		prompt_win = nil
-		prompt_buf = nil
-	end
-
-	local function submit_prompt()
-		if not prompt_buf or not vim.api.nvim_buf_is_valid(prompt_buf) then
-			close_prompt()
-			return
-		end
-		submitted = true
-		local lines = vim.api.nvim_buf_get_lines(prompt_buf, 0, -1, false)
-		local input = table.concat(lines, "\n"):gsub("^%s+", ""):gsub("%s+$", "")
-		close_prompt()
-		if input == "" then
-			logger.info("commands", "User cancelled prompt input")
-			return
-		end
-		logger.info("commands", "Processing with prompt: " .. input:sub(1, 50) .. (#input > 50 and "..." or ""))
-		local content = has_selection and (input .. "\n\nCode:\n" .. selection_text) or input
-		-- Pass captured range so scheduler/patch know where to inject the generated code
-		local prompt = {
-			content = content,
-			start_line = injection_range.start_line,
-			end_line = injection_range.end_line,
-			start_col = 1,
-			end_col = 1,
-			selection = selection,
-			user_prompt = input,
-			-- Explicit injection range (same as start_line/end_line) for downstream
-			injection_range = injection_range,
-		}
-		local autocmds = require("codetyper.adapters.nvim.autocmds")
-		autocmds.process_single_prompt(bufnr, prompt, filepath, true)
-		logger.func_exit("commands", "cmd_transform_selection", "completed")
-	end
-
-	local augroup = vim.api.nvim_create_augroup("CodetyperPrompt_" .. prompt_buf, { clear = true })
-	local submitted = false
-
-	-- Submit on :w (acwrite buffer triggers BufWriteCmd)
-	vim.api.nvim_create_autocmd("BufWriteCmd", {
-		group = augroup,
-		buffer = prompt_buf,
-		callback = function()
-			if prompt_win and vim.api.nvim_win_is_valid(prompt_win) then
-				submitted = true
-				submit_prompt()
-			end
-		end,
-	})
-
-	-- Keep focus in prompt window (prevent leaving to other buffers)
-	vim.api.nvim_create_autocmd("BufLeave", {
-		group = augroup,
-		buffer = prompt_buf,
-		callback = function()
-			if prompt_win and vim.api.nvim_win_is_valid(prompt_win) then
-				vim.api.nvim_set_current_win(prompt_win)
-			end
-		end,
-	})
-
-	-- Clean up when window is closed (e.g. :q or close button)
-	vim.api.nvim_create_autocmd("WinClosed", {
-		group = augroup,
-		pattern = tostring(prompt_win),
-		callback = function()
-			if not submitted then
-				logger.info("commands", "User cancelled prompt input")
-			end
-			close_prompt()
-		end,
-	})
-
-	local map_opts = { buffer = prompt_buf, noremap = true, silent = true }
-	-- Normal mode: Enter, :w, or Ctrl+Enter to submit
-	vim.keymap.set("n", "<CR>", submit_prompt, map_opts)
-	vim.keymap.set("n", "<C-CR>", submit_prompt, map_opts)
-	vim.keymap.set("n", "<C-Enter>", submit_prompt, map_opts)
-	vim.keymap.set("n", "<leader>w", "<cmd>w<cr>", vim.tbl_extend("force", map_opts, { desc = "Submit prompt" }))
-	-- Insert mode: Ctrl+Enter to submit
-	vim.keymap.set("i", "<C-CR>", submit_prompt, map_opts)
-	vim.keymap.set("i", "<C-Enter>", submit_prompt, map_opts)
-	-- Close/cancel: Esc (in normal), q, or :q
-	vim.keymap.set("n", "<Esc>", close_prompt, map_opts)
-	vim.keymap.set("n", "q", close_prompt, map_opts)
-
-	vim.cmd("startinsert")
-end
-
 --- Index the entire project
 local function cmd_index_project()
 	local indexer = require("codetyper.features.indexer")
@@ -627,59 +171,6 @@ local function cmd_forget(pattern)
 	end
 end
 
---- Transform a single prompt at cursor position
-local function cmd_transform_at_cursor()
-	local parser = require("codetyper.parser")
-	local autocmds = require("codetyper.adapters.nvim.autocmds")
-
-	local bufnr = vim.api.nvim_get_current_buf()
-	local filepath = vim.fn.expand("%:p")
-
-	vim.notify(
-		"[codetyper] cmd_transform_at_cursor called: bufnr=" .. bufnr .. ", filepath=" .. tostring(filepath),
-		vim.log.levels.DEBUG
-	)
-
-	if filepath == "" then
-		vim.notify("[codetyper] No file in current buffer", vim.log.levels.DEBUG)
-		utils.notify("No file in current buffer", vim.log.levels.WARN)
-		return
-	end
-
-	-- Find prompt at cursor
-	vim.notify("[codetyper] Calling parser.get_prompt_at_cursor...", vim.log.levels.DEBUG)
-	local prompt = parser.get_prompt_at_cursor(bufnr)
-	vim.notify(
-		"[codetyper] parser.get_prompt_at_cursor returned: " .. (prompt and "prompt found" or "nil"),
-		vim.log.levels.DEBUG
-	)
-
-	if not prompt then
-		vim.notify("[codetyper] No prompt found at cursor", vim.log.levels.DEBUG)
-		utils.notify("No /@ @/ tag at cursor position", vim.log.levels.WARN)
-		return
-	end
-
-	vim.notify(
-		"[codetyper] Prompt found: start_line="
-			.. prompt.start_line
-			.. ", end_line="
-			.. prompt.end_line
-			.. ", content_length="
-			.. #prompt.content,
-		vim.log.levels.DEBUG
-	)
-
-	local clean_prompt = parser.clean_prompt(prompt.content)
-	vim.notify("[codetyper] Clean prompt: " .. clean_prompt:sub(1, 50) .. "...", vim.log.levels.DEBUG)
-	utils.notify("Transforming: " .. clean_prompt:sub(1, 40) .. "...", vim.log.levels.INFO)
-
-	-- Use the same processing logic as automatic mode (skip processed check for manual mode)
-	vim.notify("[codetyper] Calling autocmds.process_single_prompt...", vim.log.levels.DEBUG)
-	autocmds.process_single_prompt(bufnr, prompt, filepath, true)
-	vim.notify("[codetyper] autocmds.process_single_prompt completed", vim.log.levels.DEBUG)
-end
-
 --- Main command dispatcher
 ---@param args table Command arguments
 --- Show LLM accuracy statistics
@@ -732,48 +223,17 @@ local function coder_cmd(args)
 	local subcommand = args.fargs[1] or "toggle"
 
 	local commands = {
-		open = cmd_open,
-		close = cmd_close,
-		toggle = cmd_toggle,
-		process = cmd_process,
-		status = cmd_status,
-		focus = cmd_focus,
 		tree = cmd_tree,
 		["tree-view"] = cmd_tree_view,
 		reset = cmd_reset,
 		gitignore = cmd_gitignore,
-
-		["transform-selection"] = cmd_transform_selection,
-
+		["transform-selection"] = transform.cmd_transform_selection,
 		["index-project"] = cmd_index_project,
 		["index-status"] = cmd_index_status,
 		memories = cmd_memories,
 		forget = function(args)
 			cmd_forget(args.fargs[2])
 		end,
-		["auto-toggle"] = function()
-			local preferences = require("codetyper.config.preferences")
-			preferences.toggle_auto_process()
-		end,
-		["auto-set"] = function(args)
-			local preferences = require("codetyper.config.preferences")
-			local arg = (args[1] or ""):lower()
-			if arg == "auto" or arg == "automatic" or arg == "on" then
-				preferences.set_auto_process(true)
-				utils.notify("Set to automatic mode", vim.log.levels.INFO)
-			elseif arg == "manual" or arg == "off" then
-				preferences.set_auto_process(false)
-				utils.notify("Set to manual mode", vim.log.levels.INFO)
-			else
-				local auto = preferences.is_auto_process_enabled()
-				if auto == nil then
-					utils.notify("Mode not set yet (will ask on first prompt)", vim.log.levels.INFO)
-				else
-					local mode = auto and "automatic" or "manual"
-					utils.notify("Currently in " .. mode .. " mode", vim.log.levels.INFO)
-				end
-			end
-		end,
 		-- LLM smart selection commands
 		["llm-stats"] = cmd_llm_stats,
 		["llm-feedback-good"] = function()
@@ -849,25 +309,17 @@ function M.setup()
 		nargs = "?",
 		complete = function()
 			return {
-				"open",
-				"close",
-				"toggle",
 				"process",
 				"status",
-				"focus",
 				"tree",
 				"tree-view",
 				"reset",
 				"gitignore",
-				"transform",
-				"transform-cursor",
 				"transform-selection",
 				"index-project",
 				"index-status",
 				"memories",
 				"forget",
-				"auto-toggle",
-				"auto-set",
 				"llm-stats",
 				"llm-feedback-good",
 				"llm-feedback-bad",
@@ -884,23 +336,6 @@ function M.setup()
 		desc = "Codetyper.nvim commands",
 	})
 
-	-- Convenience aliases
-	vim.api.nvim_create_user_command("CoderOpen", function()
-		cmd_open()
-	end, { desc = "Open Coder view" })
-
-	vim.api.nvim_create_user_command("CoderClose", function()
-		cmd_close()
-	end, { desc = "Close Coder view" })
-
-	vim.api.nvim_create_user_command("CoderToggle", function()
-		cmd_toggle()
-	end, { desc = "Toggle Coder view" })
-
-	vim.api.nvim_create_user_command("CoderProcess", function()
-		cmd_process()
-	end, { desc = "Process prompt and generate code" })
-
 	vim.api.nvim_create_user_command("CoderTree", function()
 		cmd_tree()
 	end, { desc = "Refresh tree.log" })
@@ -909,14 +344,8 @@ function M.setup()
 		cmd_tree_view()
 	end, { desc = "View tree.log" })
 
-	vim.api.nvim_create_user_command("CoderTransformVisual", function(opts)
-		local start_line = opts.line1
-		local end_line = opts.line2
-		cmd_transform_range(start_line, end_line)
-	end, { range = true, desc = "Transform /@ @/ tags in visual selection" })
-
 	vim.api.nvim_create_user_command("CoderTransformSelection", function()
-		cmd_transform_selection()
+		transform.cmd_transform_selection()
 	end, { desc = "Transform visual selection with custom prompt input" })
 
 	-- Project indexer commands
@@ -939,39 +368,6 @@ function M.setup()
 		nargs = "?",
 	})
 
-	-- Preferences commands
-	vim.api.nvim_create_user_command("CoderAutoToggle", function()
-		local preferences = require("codetyper.config.preferences")
-		preferences.toggle_auto_process()
-	end, { desc = "Toggle automatic/manual prompt processing" })
-
-	vim.api.nvim_create_user_command("CoderAutoSet", function(opts)
-		local preferences = require("codetyper.config.preferences")
-		local arg = opts.args:lower()
-		if arg == "auto" or arg == "automatic" or arg == "on" then
-			preferences.set_auto_process(true)
-			vim.notify("Codetyper: Set to automatic mode", vim.log.levels.INFO)
-		elseif arg == "manual" or arg == "off" then
-			preferences.set_auto_process(false)
-			vim.notify("Codetyper: Set to manual mode", vim.log.levels.INFO)
-		else
-			-- Show current mode
-			local auto = preferences.is_auto_process_enabled()
-			if auto == nil then
-				vim.notify("Codetyper: Mode not set yet (will ask on first prompt)", vim.log.levels.INFO)
-			else
-				local mode = auto and "automatic" or "manual"
-				vim.notify("Codetyper: Currently in " .. mode .. " mode", vim.log.levels.INFO)
-			end
-		end
-	end, {
-		desc = "Set prompt processing mode (auto/manual)",
-		nargs = "?",
-		complete = function()
-			return { "auto", "manual" }
-		end,
-	})
-
 	-- Brain feedback command - teach the brain from your experience
 	vim.api.nvim_create_user_command("CoderFeedback", function(opts)
 		local brain = require("codetyper.core.memory")
@@ -1154,17 +550,17 @@ end
 function M.setup_keymaps()
 	-- Visual mode: transform selection with custom prompt input
 	vim.keymap.set("v", "<leader>ctt", function()
-		cmd_transform_selection()
+		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()
-		cmd_transform_selection()
+		transform.cmd_transform_selection()
 	end, {
 		silent = true,
-		desc = "Coder: Transform with prompt (no selection)",
+		desc = "Coder: Open prompt window",
 	})
 end
 
diff --git a/lua/codetyper/config/defaults.lua b/lua/codetyper/config/defaults.lua
index 0ed61b2..fd0bfca 100644
--- a/lua/codetyper/config/defaults.lua
+++ b/lua/codetyper/config/defaults.lua
@@ -4,79 +4,57 @@ local M = {}
 
 ---@type CoderConfig
 local defaults = {
-  llm = {
-    provider = "ollama", -- Options: "ollama", "openai", "gemini", "copilot"
-    ollama = {
-      host = "http://localhost:11434",
-      model = "deepseek-coder:6.7b",
-    },
-    openai = {
-      api_key = nil, -- Will use OPENAI_API_KEY env var if nil
-      model = "gpt-4o",
-      endpoint = nil, -- Custom endpoint (Azure, OpenRouter, etc.)
-    },
-    gemini = {
-      api_key = nil, -- Will use GEMINI_API_KEY env var if nil
-      model = "gemini-2.0-flash",
-    },
-    copilot = {
-      model = "claude-sonnet-4", -- Uses GitHub Copilot authentication
-    },
-  },
-  window = {
-    width = 25, -- 25% of screen width (1/4)
-    position = "left",
-    border = "rounded",
-  },
-  patterns = {
-    open_tag = "/@",
-    close_tag = "@/",
-    file_pattern = "*.coder.*",
-  },
-  auto_gitignore = true,
-  auto_index = false, -- Auto-create coder companion files on file open
-  indexer = {
-    enabled = true, -- Enable project indexing
-    auto_index = true, -- Index files on save
-    index_on_open = false, -- Index project when opening
-    max_file_size = 100000, -- Skip files larger than 100KB
-    excluded_dirs = { "node_modules", "dist", "build", ".git", ".coder", "__pycache__", "vendor", "target" },
-    index_extensions = { "lua", "ts", "tsx", "js", "jsx", "py", "go", "rs", "rb", "java", "c", "cpp", "h", "hpp" },
-    memory = {
-      enabled = true, -- Enable memory persistence
-      max_memories = 1000, -- Maximum stored memories
-      prune_threshold = 0.1, -- Remove low-weight memories
-    },
-  },
-  brain = {
-    enabled = true, -- Enable brain learning system
-    auto_learn = true, -- Auto-learn from events
-    auto_commit = true, -- Auto-commit after threshold
-    commit_threshold = 10, -- Changes before auto-commit
-    max_nodes = 5000, -- Maximum nodes before pruning
-    max_deltas = 500, -- Maximum delta history
-    prune = {
-      enabled = true, -- Enable auto-pruning
-      threshold = 0.1, -- Remove nodes below this weight
-      unused_days = 90, -- Remove unused nodes after N days
-    },
-    output = {
-      max_tokens = 4000, -- Token budget for LLM context
-      format = "compact", -- "compact"|"json"|"natural"
-    },
-  },
-  suggestion = {
-    enabled = true, -- Enable ghost text suggestions (Copilot-style)
-    auto_trigger = true, -- Auto-trigger on typing
-    debounce = 150, -- Debounce in milliseconds
-    use_copilot = true, -- Use copilot.lua suggestions when available, fallback to codetyper
-    keymap = {
-      accept = "<Tab>", -- Accept suggestion
-      next = "<M-]>", -- Next suggestion (Alt+])
-      prev = "<M-[>", -- Previous suggestion (Alt+[)
-      dismiss = "<C-]>", -- Dismiss suggestion (Ctrl+])
-    },
-  },
+	llm = {
+		provider = "ollama", -- Options: "ollama", "openai", "gemini", "copilot"
+		ollama = {
+			host = "http://localhost:11434",
+			model = "deepseek-coder:6.7b",
+		},
+		openai = {
+			api_key = nil, -- Will use OPENAI_API_KEY env var if nil
+			model = "gpt-4o",
+			endpoint = nil, -- Custom endpoint (Azure, OpenRouter, etc.)
+		},
+		gemini = {
+			api_key = nil, -- Will use GEMINI_API_KEY env var if nil
+			model = "gemini-2.0-flash",
+		},
+		copilot = {
+			model = "claude-sonnet-4", -- Uses GitHub Copilot authentication
+		},
+	},
+	auto_gitignore = true,
+	auto_index = false, -- Auto-create coder companion files on file open
+	indexer = {
+		enabled = true, -- Enable project indexing
+		auto_index = true, -- Index files on save
+		index_on_open = false, -- Index project when opening
+		max_file_size = 100000, -- Skip files larger than 100KB
+		excluded_dirs = { "node_modules", "dist", "build", ".git", ".coder", "__pycache__", "vendor", "target" },
+		index_extensions = { "lua", "ts", "tsx", "js", "jsx", "py", "go", "rs", "rb", "java", "c", "cpp", "h", "hpp" },
+		memory = {
+			enabled = true, -- Enable memory persistence
+			max_memories = 1000, -- Maximum stored memories
+			prune_threshold = 0.1, -- Remove low-weight memories
+		},
+	},
+	brain = {
+		enabled = true, -- Enable brain learning system
+		auto_learn = true, -- Auto-learn from events
+		auto_commit = true, -- Auto-commit after threshold
+		commit_threshold = 10, -- Changes before auto-commit
+		max_nodes = 5000, -- Maximum nodes before pruning
+		max_deltas = 500, -- Maximum delta history
+		prune = {
+			enabled = true, -- Enable auto-pruning
+			threshold = 0.1, -- Remove nodes below this weight
+			unused_days = 90, -- Remove unused nodes after N days
+		},
+		output = {
+			max_tokens = 4000, -- Token budget for LLM context
+			format = "compact", -- "compact"|"json"|"natural"
+		},
+	},
 }
 
 --- Deep merge two tables
@@ -84,68 +62,68 @@ local defaults = {
 ---@param t2 table Table to merge into base
 ---@return table Merged table
 local function deep_merge(t1, t2)
-  local result = vim.deepcopy(t1)
-  for k, v in pairs(t2) do
-    if type(v) == "table" and type(result[k]) == "table" then
-      result[k] = deep_merge(result[k], v)
-    else
-      result[k] = v
-    end
-  end
-  return result
+	local result = vim.deepcopy(t1)
+	for k, v in pairs(t2) do
+		if type(v) == "table" and type(result[k]) == "table" then
+			result[k] = deep_merge(result[k], v)
+		else
+			result[k] = v
+		end
+	end
+	return result
 end
 
 --- Setup configuration with user options
 ---@param opts? CoderConfig User configuration options
 ---@return CoderConfig Final configuration
 function M.setup(opts)
-  opts = opts or {}
-  return deep_merge(defaults, opts)
+	opts = opts or {}
+	return deep_merge(defaults, opts)
 end
 
 --- Get default configuration
 ---@return CoderConfig Default configuration
 function M.get_defaults()
-  return vim.deepcopy(defaults)
+	return vim.deepcopy(defaults)
 end
 
 --- Validate configuration
 ---@param config CoderConfig Configuration to validate
 ---@return boolean, string? Valid status and optional error message
 function M.validate(config)
-  if not config.llm then
-    return false, "Missing LLM configuration"
-  end
+	if not config.llm then
+		return false, "Missing LLM configuration"
+	end
 
-  local valid_providers = { "ollama", "openai", "gemini", "copilot" }
-  local is_valid_provider = false
-  for _, p in ipairs(valid_providers) do
-    if config.llm.provider == p then
-      is_valid_provider = true
-      break
-    end
-  end
+	local valid_providers = { "ollama", "openai", "gemini", "copilot" }
+	local is_valid_provider = false
+	for _, p in ipairs(valid_providers) do
+		if config.llm.provider == p then
+			is_valid_provider = true
+			break
+		end
+	end
 
-  if not is_valid_provider then
-    return false, "Invalid LLM provider. Must be one of: " .. table.concat(valid_providers, ", ")
-  end
+	if not is_valid_provider then
+		return false, "Invalid LLM provider. Must be one of: " .. table.concat(valid_providers, ", ")
+	end
 
-  -- Validate provider-specific configuration
-  if config.llm.provider == "openai" then
-    local api_key = config.llm.openai.api_key or vim.env.OPENAI_API_KEY
-    if not api_key or api_key == "" then
-      return false, "OpenAI API key not configured. Set llm.openai.api_key or OPENAI_API_KEY env var"
-    end
-  elseif config.llm.provider == "gemini" then
-    local api_key = config.llm.gemini.api_key or vim.env.GEMINI_API_KEY
-    if not api_key or api_key == "" then
-      return false, "Gemini API key not configured. Set llm.gemini.api_key or GEMINI_API_KEY env var"
-    end
-  end
-  -- Note: copilot uses OAuth from copilot.lua/copilot.vim, validated at runtime
-  -- Note: ollama doesn't require API key, just host configuration
+	-- Validate provider-specific configuration
+	if config.llm.provider == "openai" then
+		local api_key = config.llm.openai.api_key or vim.env.OPENAI_API_KEY
+		if not api_key or api_key == "" then
+			return false, "OpenAI API key not configured. Set llm.openai.api_key or OPENAI_API_KEY env var"
+		end
+	elseif config.llm.provider == "gemini" then
+		local api_key = config.llm.gemini.api_key or vim.env.GEMINI_API_KEY
+		if not api_key or api_key == "" then
+			return false, "Gemini API key not configured. Set llm.gemini.api_key or GEMINI_API_KEY env var"
+		end
+	end
+	-- Note: copilot uses OAuth from copilot.lua/copilot.vim, validated at runtime
+	-- Note: ollama doesn't require API key, just host configuration
 
-  return true
+	return true
 end
 
 return M
diff --git a/lua/codetyper/core/diff/patch.lua b/lua/codetyper/core/diff/patch.lua
index 2d0b477..41a4ff2 100644
--- a/lua/codetyper/core/diff/patch.lua
+++ b/lua/codetyper/core/diff/patch.lua
@@ -233,8 +233,24 @@ function M.create_from_event(event, generated_code, confidence, strategy)
 	local injection_strategy = strategy
 	local injection_range = nil
 
+	-- Handle intent_override from transform-selection (e.g., cursor insert mode)
+	if event.intent_override and event.intent_override.action then
+		injection_strategy = event.intent_override.action
+		-- Use injection_range from transform-selection, not event.range
+		injection_range = event.injection_range or (event.range and {
+			start_line = event.range.start_line,
+			end_line = event.range.end_line,
+		})
+		pcall(function()
+			local logs = require("codetyper.adapters.nvim.ui.logs")
+			logs.add({
+				type = "info",
+				message = string.format("Using override strategy: %s (%s)", injection_strategy,
+					injection_range and (injection_range.start_line .. "-" .. injection_range.end_line) or "nil"),
+			})
+		end)
 	-- If we have SEARCH/REPLACE blocks, use that strategy
-	if use_search_replace then
+	elseif use_search_replace then
 		injection_strategy = "search_replace"
 		pcall(function()
 			local logs = require("codetyper.adapters.nvim.ui.logs")
@@ -519,14 +535,18 @@ local function remove_prompt_tags(bufnr)
 	return removed
 end
 
---- Check if it's safe to modify the buffer (not in insert mode)
+--- Check if it's safe to modify the buffer (not in insert or visual mode)
 ---@return boolean
 local function is_safe_to_modify()
 	local mode = vim.fn.mode()
-	-- Don't modify if in insert mode or completion is visible
+	-- Don't modify if in insert mode, visual mode, or completion is visible
 	if mode == "i" or mode == "ic" or mode == "ix" then
 		return false
 	end
+	-- Visual modes: v (char), V (line), \22 (block)
+	if mode == "v" or mode == "V" or mode == "\22" then
+		return false
+	end
 	if vim.fn.pumvisible() == 1 then
 		return false
 	end
@@ -540,9 +560,9 @@ end
 function M.apply(patch)
 	logger.info("patch", string.format("apply() entered: id=%s strategy=%s has_range=%s", patch.id, tostring(patch.injection_strategy), patch.injection_range and "yes" or "no"))
 
-	-- Check if safe to modify (not in insert mode)
+	-- Check if safe to modify (not in insert or visual mode)
 	if not is_safe_to_modify() then
-		logger.info("patch", "apply aborted: user_typing (insert mode or pum visible)")
+		logger.info("patch", "apply aborted: not safe (insert/visual mode or pum visible)")
 		return false, "user_typing"
 	end
 
diff --git a/lua/codetyper/core/scheduler/scheduler.lua b/lua/codetyper/core/scheduler/scheduler.lua
index 3511f02..df5721c 100644
--- a/lua/codetyper/core/scheduler/scheduler.lua
+++ b/lua/codetyper/core/scheduler/scheduler.lua
@@ -59,6 +59,13 @@ function M.is_insert_mode()
 	return mode == "i" or mode == "ic" or mode == "ix"
 end
 
+--- Check if we're in visual mode
+---@return boolean
+function M.is_visual_mode()
+	local mode = vim.fn.mode()
+	return mode == "v" or mode == "V" or mode == "\22"
+end
+
 --- Check if it's safe to inject code
 ---@return boolean
 ---@return string|nil reason if not safe
@@ -71,6 +78,10 @@ function M.is_safe_to_inject()
 		return false, "insert_mode"
 	end
 
+	if M.is_visual_mode() then
+		return false, "visual_mode"
+	end
+
 	return true, nil
 end
 
@@ -503,6 +514,13 @@ function M.schedule_patch_flush()
 			if not waiting_to_flush then
 				waiting_to_flush = true
 				logger.info("scheduler", "Waiting for user to finish typing before applying code...")
+				-- Notify user about the wait
+				local utils = require("codetyper.support.utils")
+				if reason == "visual_mode" then
+					utils.notify("Queue waiting: exit Visual mode to inject code", vim.log.levels.INFO)
+				elseif reason == "insert_mode" then
+					utils.notify("Queue waiting: exit Insert mode to inject code", vim.log.levels.INFO)
+				end
 			end
 			-- Retry after a delay - keep waiting for user to finish typing
 			M.schedule_patch_flush()
@@ -549,6 +567,20 @@ local function setup_autocmds()
 		desc = "Flush pending patches on InsertLeave",
 	})
 
+	-- Flush patches when leaving visual mode
+	vim.api.nvim_create_autocmd("ModeChanged", {
+		group = augroup,
+		pattern = "[vV\x16]*:*", -- visual mode to any other mode
+		callback = function()
+			vim.defer_fn(function()
+				if not M.is_insert_mode() and not M.is_completion_visible() then
+					patch.flush_pending_smart()
+				end
+			end, state.config.completion_delay_ms)
+		end,
+		desc = "Flush pending patches on VisualLeave",
+	})
+
 	-- Flush patches on cursor hold
 	vim.api.nvim_create_autocmd("CursorHold", {
 		group = augroup,
diff --git a/lua/codetyper/core/transform.lua b/lua/codetyper/core/transform.lua
new file mode 100644
index 0000000..5cf16d5
--- /dev/null
+++ b/lua/codetyper/core/transform.lua
@@ -0,0 +1,224 @@
+local M = {}
+
+--- Return editor dimensions (from UI, like 99 plugin)
+---@return number width
+---@return number height
+local function get_ui_dimensions()
+	local ui = vim.api.nvim_list_uis()[1]
+	if ui then
+		return ui.width, ui.height
+	end
+	return vim.o.columns, vim.o.lines
+end
+
+--- Centered floating window config for prompt (2/3 width, 1/3 height)
+---@return table { width, height, row, col, border }
+local function create_centered_window()
+	local width, height = get_ui_dimensions()
+	local win_width = math.floor(width * 2 / 3)
+	local win_height = math.floor(height / 3)
+	return {
+		width = win_width,
+		height = win_height,
+		row = math.floor((height - win_height) / 2),
+		col = math.floor((width - win_width) / 2),
+		border = "rounded",
+	}
+end
+
+--- Get visual selection text and range
+---@return table|nil { text: string, start_line: number, end_line: number }
+local function get_visual_selection()
+	local mode = vim.api.nvim_get_mode().mode
+	-- Check if in visual mode
+	local is_visual = mode == "v" or mode == "V" or mode == "\22"
+	if not is_visual then
+		return nil
+	end
+	-- Get selection range BEFORE any mode changes
+	local start_line = vim.fn.line("'<")
+	local end_line = vim.fn.line("'>")
+	-- Check if marks are valid (might be 0 if not in visual mode)
+	if start_line <= 0 or end_line <= 0 then
+		return nil
+	end
+	-- Third argument must be a Vim dictionary; empty Lua table can be treated as list
+	local opts = { type = mode }
+	local selection = vim.fn.getregion(vim.fn.getpos("'<"), vim.fn.getpos("'>"), opts)
+	local text = type(selection) == "table" and table.concat(selection, "\n") or tostring(selection or "")
+	return {
+		text = text,
+		start_line = start_line,
+		end_line = end_line,
+	}
+end
+
+--- Transform visual selection with custom prompt input
+--- Opens input window for prompt, processes selection on confirm.
+--- When nothing is selected (e.g. from Normal mode), only the prompt is requested.
+function M.cmd_transform_selection()
+	local logger = require("codetyper.support.logger")
+	logger.func_entry("commands", "cmd_transform_selection", {})
+	-- Get visual selection (returns table with text, start_line, end_line or nil)
+	local selection_data = get_visual_selection()
+	local selection_text = selection_data and selection_data.text or ""
+	local has_selection = selection_text and #selection_text >= 4
+
+	local bufnr = vim.api.nvim_get_current_buf()
+	local filepath = vim.fn.expand("%:p")
+	local line_count = vim.api.nvim_buf_line_count(bufnr)
+	line_count = math.max(1, line_count)
+
+	-- Range for injection: selection, cursor line when no selection
+	local start_line, end_line
+	local is_cursor_insert = false
+	if has_selection and selection_data then
+		start_line = selection_data.start_line
+		end_line = selection_data.end_line
+		logger.info("commands", string.format("Visual selection: start=%d end=%d selected_text_lines=%d",
+			start_line, end_line, #vim.split(selection_text, "\n", { plain = true })))
+	else
+		-- No selection: insert at current cursor line (not replace whole file)
+		start_line = vim.fn.line(".")
+		end_line = start_line
+		is_cursor_insert = true
+	end
+	-- Clamp to valid 1-based range (avoid 0 or out-of-bounds)
+	start_line = math.max(1, math.min(start_line, line_count))
+	end_line = math.max(1, math.min(end_line, line_count))
+	if end_line < start_line then
+		end_line = start_line
+	end
+
+	-- Capture injection range so we know exactly where to apply the generated code later
+	local injection_range = { start_line = start_line, end_line = end_line }
+	local range_line_count = end_line - start_line + 1
+
+	-- Open centered prompt window (pattern from 99: acwrite + BufWriteCmd to submit, BufLeave to keep focus)
+	local prompt_buf = vim.api.nvim_create_buf(false, true)
+	vim.bo[prompt_buf].buftype = "acwrite"
+	vim.bo[prompt_buf].bufhidden = "wipe"
+	vim.bo[prompt_buf].filetype = "markdown"
+	vim.bo[prompt_buf].swapfile = false
+	vim.api.nvim_buf_set_name(prompt_buf, "codetyper-prompt")
+
+	local win_opts = create_centered_window()
+	local prompt_win = vim.api.nvim_open_win(prompt_buf, true, {
+		relative = "editor",
+		row = win_opts.row,
+		col = win_opts.col,
+		width = win_opts.width,
+		height = win_opts.height,
+		style = "minimal",
+		border = win_opts.border,
+		title = has_selection and " Enter prompt for selection " or " Enter prompt ",
+		title_pos = "center",
+	})
+	vim.wo[prompt_win].wrap = true
+	vim.api.nvim_set_current_win(prompt_win)
+
+	local function close_prompt()
+		if prompt_win and vim.api.nvim_win_is_valid(prompt_win) then
+			vim.api.nvim_win_close(prompt_win, true)
+		end
+		if prompt_buf and vim.api.nvim_buf_is_valid(prompt_buf) then
+			vim.api.nvim_buf_delete(prompt_buf, { force = true })
+		end
+		prompt_win = nil
+		prompt_buf = nil
+	end
+
+	local submitted = false
+
+	local function submit_prompt()
+		if not prompt_buf or not vim.api.nvim_buf_is_valid(prompt_buf) then
+			close_prompt()
+			return
+		end
+		submitted = true
+		local lines = vim.api.nvim_buf_get_lines(prompt_buf, 0, -1, false)
+		local input = table.concat(lines, "\n"):gsub("^%s+", ""):gsub("%s+$", "")
+		close_prompt()
+		if input == "" then
+			logger.info("commands", "User cancelled prompt input")
+			return
+		end
+		local content
+		if has_selection then
+			content = input .. "\n\nCode to replace (replace this code):\n" .. selection_text
+		elseif is_cursor_insert then
+			content = "Insert at line " .. start_line .. ":\n" .. input
+		else
+			content = input
+		end
+		-- Pass captured range so scheduler/patch know where to inject the generated code
+		local prompt = {
+			content = content,
+			start_line = injection_range.start_line,
+			end_line = injection_range.end_line,
+			start_col = 1,
+			end_col = 1,
+			user_prompt = input,
+			-- Explicit injection range (same as start_line/end_line) for downstream
+			injection_range = injection_range,
+			-- When there's a selection, force replace; when no selection, insert at cursor
+			intent_override = has_selection and { action = "replace" } or (is_cursor_insert and { action = "insert" } or nil),
+		}
+		local autocmds = require("codetyper.adapters.nvim.autocmds")
+		autocmds.process_single_prompt(bufnr, prompt, filepath, true)
+	end
+
+	local augroup = vim.api.nvim_create_augroup("CodetyperPrompt_" .. prompt_buf, { clear = true })
+
+	-- Submit on :w (acwrite buffer triggers BufWriteCmd)
+	vim.api.nvim_create_autocmd("BufWriteCmd", {
+		group = augroup,
+		buffer = prompt_buf,
+		callback = function()
+			if prompt_win and vim.api.nvim_win_is_valid(prompt_win) then
+				submitted = true
+				submit_prompt()
+			end
+		end,
+	})
+
+	-- Keep focus in prompt window (prevent leaving to other buffers)
+	vim.api.nvim_create_autocmd("BufLeave", {
+		group = augroup,
+		buffer = prompt_buf,
+		callback = function()
+			if prompt_win and vim.api.nvim_win_is_valid(prompt_win) then
+				vim.api.nvim_set_current_win(prompt_win)
+			end
+		end,
+	})
+
+	-- Clean up when window is closed (e.g. :q or close button)
+	vim.api.nvim_create_autocmd("WinClosed", {
+		group = augroup,
+		pattern = tostring(prompt_win),
+		callback = function()
+			if not submitted then
+				logger.info("commands", "User cancelled prompt input")
+			end
+			close_prompt()
+		end,
+	})
+
+	local map_opts = { buffer = prompt_buf, noremap = true, silent = true }
+	-- Normal mode: Enter, :w, or Ctrl+Enter to submit
+	vim.keymap.set("n", "<CR>", submit_prompt, map_opts)
+	vim.keymap.set("n", "<C-CR>", submit_prompt, map_opts)
+	vim.keymap.set("n", "<C-Enter>", submit_prompt, map_opts)
+	vim.keymap.set("n", "<leader>w", "<cmd>w<cr>", vim.tbl_extend("force", map_opts, { desc = "Submit prompt" }))
+	-- Insert mode: Ctrl+Enter to submit
+	vim.keymap.set("i", "<C-CR>", submit_prompt, map_opts)
+	vim.keymap.set("i", "<C-Enter>", submit_prompt, map_opts)
+	-- Close/cancel: Esc (in normal), q, or :q
+	vim.keymap.set("n", "<Esc>", close_prompt, map_opts)
+	vim.keymap.set("n", "q", close_prompt, map_opts)
+
+	vim.cmd("startinsert")
+end
+
+return M
diff --git a/lua/codetyper/init.lua b/lua/codetyper/init.lua
index 5d9d32c..b7f9908 100644
--- a/lua/codetyper/init.lua
+++ b/lua/codetyper/init.lua
@@ -18,66 +18,66 @@ M._initialized = false
 --- Setup the plugin with user configuration
 ---@param opts? CoderConfig User configuration options
 function M.setup(opts)
-  if M._initialized then
-    return
-  end
+	if M._initialized then
+		return
+	end
 
-  local config = require("codetyper.config.defaults")
-  M.config = config.setup(opts)
+	local config = require("codetyper.config.defaults")
+	M.config = config.setup(opts)
 
-  -- Initialize modules
-  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")
+	-- Initialize modules
+	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")
 
-  -- Register commands
-  commands.setup()
+	-- Register commands
+	commands.setup()
 
-  -- Setup autocommands
-  autocmds.setup()
+	-- Setup autocommands
+	autocmds.setup()
 
-  -- Setup file reference completion
-  completion.setup()
+	-- Setup file reference completion
+	completion.setup()
 
-  -- Ensure .gitignore has coder files excluded
-  gitignore.ensure_ignored()
+	-- Ensure .gitignore has coder files excluded
+	gitignore.ensure_ignored()
 
-  -- Initialize tree logging (creates .coder folder and initial tree.log)
-  tree.setup()
+	-- Initialize tree logging (creates .coder folder and initial tree.log)
+	tree.setup()
 
-  -- Initialize project indexer if enabled
-  if M.config.indexer and M.config.indexer.enabled then
-    local indexer = require("codetyper.features.indexer")
-    indexer.setup(M.config.indexer)
-  end
+	-- Initialize project indexer if enabled
+	if M.config.indexer and M.config.indexer.enabled then
+		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.core.memory")
-    brain.setup(M.config.brain)
-  end
+	-- Initialize brain learning system if enabled
+	if M.config.brain and M.config.brain.enabled then
+		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.features.completion.suggestion")
-    suggestion.setup(M.config.suggestion)
-  end
+	-- Setup inline ghost text suggestions (Copilot-style)
+	if M.config.suggestion and M.config.suggestion.enabled then
+		local suggestion = require("codetyper.features.completion.suggestion")
+		suggestion.setup(M.config.suggestion)
+	end
 
-  M._initialized = true
+	M._initialized = true
 end
 
 --- Get current configuration
 ---@return CoderConfig
 function M.get_config()
-  return M.config
+	return M.config
 end
 
 --- Check if plugin is initialized
 ---@return boolean
 function M.is_initialized()
-  return M._initialized
+	return M._initialized
 end
 
 return M
diff --git a/tests/spec/config_spec.lua b/tests/spec/config_spec.lua
index 24606b6..4d0207f 100644
--- a/tests/spec/config_spec.lua
+++ b/tests/spec/config_spec.lua
@@ -12,18 +12,6 @@ describe("config", function()
 			assert.equals("claude", defaults.llm.provider)
 		end)
 
-		it("should have window configuration", function()
-			assert.is_table(defaults.window)
-			assert.equals(25, defaults.window.width)
-			assert.equals("left", defaults.window.position)
-		end)
-
-		it("should have pattern configuration", function()
-			assert.is_table(defaults.patterns)
-			assert.equals("/@", defaults.patterns.open_tag)
-			assert.equals("@/", defaults.patterns.close_tag)
-		end)
-
 		it("should have scheduler configuration", function()
 			assert.is_table(defaults.scheduler)
 			assert.is_boolean(defaults.scheduler.enabled)