diff --git a/.chatgpt_config.yaml b/.chatgpt_config.yaml
index d0ad42b..c34dc1a 100644
--- a/.chatgpt_config.yaml
+++ b/.chatgpt_config.yaml
@@ -1,27 +1,17 @@
 project_name: "chatgpt_nvim"
 default_prompt_blocks:
   - "basic-prompt"
-  - "secure-coding"
+  - "workflow-prompt"
+directories:
+  - "."
 initial_files:
   - "README.md"
-
 debug: false
-improved_debug: false
-
 preview_changes: false
 interactive_file_selection: false
 partial_acceptance: false
-
+improved_debug: false
 enable_debug_commands: true
-prompt_char_limit: 300000
+token_limit: 128000
 enable_chunking: false
 enable_step_by_step: true
-auto_lint: true
-
-# New tool auto-accept config
-tool_auto_accept:
-  readFile: false
-  editFile: false
-  executeCommand: false
-  # If you set any of these to true, it will auto accept them without prompting.
-  # 'executeCommand' should remain false by default unless you're certain it's safe.
diff --git a/README.md b/README.md
index e613435..dfb19be 100644
--- a/README.md
+++ b/README.md
@@ -83,18 +83,3 @@ commands:
 The **list** command now uses the Linux `ls` command to list directory contents. The **grep** command searches for a given pattern in a file or all files in a directory.
 
 Enjoy your improved, more flexible ChatGPT Neovim plugin with step-by-step support!
-
-## Test when developing
-add new plugin to runtimepath
-```vim
-:set rtp^=~/temp_plugins/chatgpt.vim
-```
-Clear Lua module cache
-```vim
-:lua for k in pairs(package.loaded) do if k:match("^chatgpt_nvim") then package.loaded[k]=nil end end
-```
-Load new plugin code
-```vim
-:runtime plugin/chatgpt.vim
-```
-
diff --git a/lua/chatgpt_nvim/config.lua b/lua/chatgpt_nvim/config.lua
index 2bd541f..e239044 100644
--- a/lua/chatgpt_nvim/config.lua
+++ b/lua/chatgpt_nvim/config.lua
@@ -40,6 +40,7 @@ function M.load()
     initial_prompt = "",
     directories = { "." },
     default_prompt_blocks = {},
+    -- Changed default from 128000 to 16384 as requested
     prompt_char_limit = 300000,
     project_name = "",
     debug = false,
@@ -49,17 +50,9 @@ function M.load()
     partial_acceptance = false,
     improved_debug = false,
     enable_chunking = false,
+    -- New default for step-by-step
     enable_step_by_step = true,
-
-    -- If auto_lint is true, we only do LSP-based checks.
-    auto_lint = false,
-
-    tool_auto_accept = {
-      readFile = false,
-      editFile = false,
-      replace_in_file = false,
-      executeCommand = false,
-    }
+    enable_debug_commands = false
   }
 
   if fd then
@@ -105,21 +98,12 @@ function M.load()
         if type(result.enable_chunking) == "boolean" then
           config.enable_chunking = result.enable_chunking
         end
+        -- Added logic to load enable_step_by_step from user config
         if type(result.enable_step_by_step) == "boolean" then
           config.enable_step_by_step = result.enable_step_by_step
         end
-
-        -- auto_lint controls whether we do LSP-based checks
-        if type(result.auto_lint) == "boolean" then
-          config.auto_lint = result.auto_lint
-        end
-
-        if type(result.tool_auto_accept) == "table" then
-          for k, v in pairs(result.tool_auto_accept) do
-            if config.tool_auto_accept[k] ~= nil and type(v) == "boolean" then
-              config.tool_auto_accept[k] = v
-            end
-          end
+        if type(result.enable_debug_commands) == "boolean" then
+          config.enable_debug_commands = result.enable_debug_commands
         end
       end
     end
@@ -127,7 +111,7 @@ function M.load()
     config.initial_prompt = "You are a coding assistant who receives a project's context and user instructions..."
   end
 
-  -- Merge default prompt blocks
+  -- Merge the default prompt blocks with the config's initial prompt
   if type(config.default_prompt_blocks) == "table" and #config.default_prompt_blocks > 0 then
     local merged_prompt = {}
     for _, block_name in ipairs(config.default_prompt_blocks) do
diff --git a/lua/chatgpt_nvim/init.lua b/lua/chatgpt_nvim/init.lua
index 2ea41c3..8a7ab88 100644
--- a/lua/chatgpt_nvim/init.lua
+++ b/lua/chatgpt_nvim/init.lua
@@ -6,14 +6,8 @@ local config = require('chatgpt_nvim.config')
 local ui = require('chatgpt_nvim.ui')
 local prompts = require('chatgpt_nvim.prompts')
 
-local tools_manager = require("chatgpt_nvim.tools.manager")
-local tools_module = require("chatgpt_nvim.tools")
-
 local ok_yaml, lyaml = pcall(require, "lyaml")
 
-------------------------------------------------------------------------------
--- UTILITIES
-------------------------------------------------------------------------------
 local function copy_to_clipboard(text)
   vim.fn.setreg('+', text)
 end
@@ -54,6 +48,19 @@ local function read_file(path)
   return data
 end
 
+local function is_directory(path)
+  local stat = vim.loop.fs_stat(path)
+  return stat and stat.type == "directory"
+end
+
+local function handle_step_by_step_if_needed(prompt, conf)
+  local length = #prompt
+  if not conf.enable_step_by_step or length <= (conf.prompt_char_limit or 8000) then
+    return { prompt }
+  end
+  return { prompts["step-prompt"] }
+end
+
 local function close_existing_buffer_by_name(pattern)
   for _, b in ipairs(vim.api.nvim_list_bufs()) do
     local name = vim.api.nvim_buf_get_name(b)
@@ -63,98 +70,265 @@ local function close_existing_buffer_by_name(pattern)
   end
 end
 
-------------------------------------------------------------------------------
--- PROMPT CONSTRUCTION
-------------------------------------------------------------------------------
-local function build_tools_available_block()
-  local lines = {}
-  lines[#lines+1] = "<tools_available>"
-  for _, t in ipairs(tools_module.available_tools) do
-    lines[#lines+1] = string.format("- **%s**: %s\n  Usage: %s",
-      t.name, t.explanation, t.usage
-    )
-  end
-  lines[#lines+1] = "</tools_available>"
-  return table.concat(lines, "\n")
-end
-
-local function build_prompt(user_input, dirs, conf)
-  local root = vim.fn.getcwd()
-  local initial_files = conf.initial_files or {}
-  local final_sections = {}
-
-  -- 1) <initial_prompts>
-  if conf.initial_prompt and conf.initial_prompt ~= "" then
-    table.insert(final_sections, "<initial_prompts>\n" .. conf.initial_prompt .. "\n</initial_prompts>\n")
-  end
-
-  -- 2) <tools_available>
-  table.insert(final_sections, build_tools_available_block())
-
-  -- 3) <task>
-  local task_lines = {}
-  task_lines[#task_lines+1] = "<task>"
-  task_lines[#task_lines+1] = user_input
-  for _, file_path in ipairs(initial_files) do
-    task_lines[#task_lines+1] = ("'%s' (see below for file content)"):format(file_path)
-  end
-  task_lines[#task_lines+1] = "</task>\n"
-  table.insert(final_sections, table.concat(task_lines, "\n"))
-
-  -- 4) <file_content path="...">
-  local file_content_blocks = {}
-  for _, file_path in ipairs(initial_files) do
-    local full_path = root .. "/" .. file_path
-    if is_subpath(root, full_path) then
-      local fdata = read_file(full_path)
-      if fdata then
-        file_content_blocks[#file_content_blocks+1] = string.format(
-          "<file_content path=\"%s\">\n%s\n</file_content>", file_path, fdata
-        )
+local function preview_changes(changes, conf)
+  close_existing_buffer_by_name("ChatGPT_Changes_Preview$")
+  local bufnr = vim.api.nvim_create_buf(false, true)
+  vim.api.nvim_buf_set_name(bufnr, "ChatGPT_Changes_Preview")
+  vim.api.nvim_buf_set_option(bufnr, "filetype", "diff")
+  vim.api.nvim_buf_set_lines(bufnr, 0, -1, false, {
+    "# Preview of Changes:",
+    "# (Close this window to apply changes or use :q to cancel)",
+    ""
+  })
+  for _, fileinfo in ipairs(changes) do
+    local indicator = (fileinfo.delete == true) and "Delete file" or "Write file"
+    vim.api.nvim_buf_set_lines(bufnr, -1, -1, false, {
+      string.format("=== %s: %s ===", indicator, fileinfo.path or "<no path>")
+    })
+    if fileinfo.content then
+      local lines = vim.split(fileinfo.content, "\n")
+      for _, line in ipairs(lines) do
+        vim.api.nvim_buf_set_lines(bufnr, -1, -1, false, { line })
       end
     end
-  end
-  if #file_content_blocks > 0 then
-    table.insert(final_sections, table.concat(file_content_blocks, "\n\n"))
+    vim.api.nvim_buf_set_lines(bufnr, -1, -1, false, { "" })
   end
 
-  -- 5) <environment_details>
-  local env_lines = {}
-  env_lines[#env_lines+1] = "<environment_details>"
-  env_lines[#env_lines+1] = "# VSCode Visible Files"
-  for _, f in ipairs(initial_files) do
-    env_lines[#env_lines+1] = f
-  end
-  env_lines[#env_lines+1] = ""
-  env_lines[#env_lines+1] = "# VSCode Open Tabs"
-  env_lines[#env_lines+1] = "..."
-  env_lines[#env_lines+1] = ""
-  env_lines[#env_lines+1] = "# Current Time"
-  env_lines[#env_lines+1] = os.date("%x, %X (%Z)")
-  env_lines[#env_lines+1] = ""
-  env_lines[#env_lines+1] = "# Current Working Directory (" .. root .. ") Files"
-  env_lines[#env_lines+1] = context.get_project_structure(dirs, conf) or ""
-  env_lines[#env_lines+1] = ""
-  env_lines[#env_lines+1] = "# Current Mode"
-  env_lines[#env_lines+1] = "ACT MODE"
-  env_lines[#env_lines+1] = "</environment_details>"
-  table.insert(final_sections, table.concat(env_lines, "\n"))
-
-  return table.concat(final_sections, "\n\n")
+  vim.cmd("vsplit")
+  vim.cmd("buffer " .. bufnr)
 end
 
-local function handle_step_by_step_if_needed(prompt, conf)
-  local length = #prompt
-  local limit = conf.prompt_char_limit or 8000
-  if (not conf.enable_step_by_step) or (length <= limit) then
-    return { prompt }
+local function partial_accept(changes, conf)
+  close_existing_buffer_by_name("ChatGPT_Partial_Accept$")
+  local bufnr = vim.api.nvim_create_buf(false, true)
+  vim.api.nvim_buf_set_name(bufnr, "ChatGPT_Partial_Accept")
+  vim.api.nvim_buf_set_option(bufnr, "filetype", "diff")
+
+  local lines = {
+    "# Remove or comment out (prepend '#') any changes you do NOT want, then :wq, :x, or :bd to finalize partial acceptance",
+    ""
+  }
+  for _, fileinfo in ipairs(changes) do
+    local action = (fileinfo.delete == true) and "[DELETE]" or "[WRITE]"
+    table.insert(lines, string.format("%s %s", action, fileinfo.path or "<no path>"))
+    if fileinfo.content then
+      local content_lines = vim.split(fileinfo.content, "\n")
+      for _, cl in ipairs(content_lines) do
+        table.insert(lines, "  " .. cl)
+      end
+    end
+    table.insert(lines, "")
+  end
+
+  vim.api.nvim_buf_set_lines(bufnr, 0, -1, false, lines)
+
+  local final_changes = {}
+  local function on_write()
+    local edited_lines = vim.api.nvim_buf_get_lines(bufnr, 0, -1, false)
+    local keep_current = false
+    local current_fileinfo = { path = nil, content = nil, delete = false }
+    local content_accum = {}
+
+    for _, line in ipairs(edited_lines) do
+      if line:match("^#") or line == "" then
+        goto continue
+      end
+      local del_match = line:match("^%[DELETE%] (.+)")
+      local write_match = line:match("^%[WRITE%] (.+)")
+      if del_match then
+        if keep_current and (current_fileinfo.path ~= nil) then
+          if #content_accum > 0 then
+            current_fileinfo.content = table.concat(content_accum, "\n")
+          end
+          table.insert(final_changes, current_fileinfo)
+        end
+        keep_current = true
+        current_fileinfo = { path = del_match, delete = true, content = nil }
+        content_accum = {}
+      elseif write_match then
+        if keep_current and (current_fileinfo.path ~= nil) then
+          if #content_accum > 0 then
+            current_fileinfo.content = table.concat(content_accum, "\n")
+          end
+          table.insert(final_changes, current_fileinfo)
+        end
+        keep_current = true
+        current_fileinfo = { path = write_match, delete = false, content = nil }
+        content_accum = {}
+      else
+        if keep_current then
+          table.insert(content_accum, line:gsub("^%s*", ""))
+        end
+      end
+      ::continue::
+    end
+
+    if keep_current and (current_fileinfo.path ~= nil) then
+      if #content_accum > 0 then
+        current_fileinfo.content = table.concat(content_accum, "\n")
+      end
+      table.insert(final_changes, current_fileinfo)
+    end
+
+    vim.api.nvim_buf_set_option(bufnr, "modified", false)
+  end
+
+  vim.api.nvim_create_autocmd("BufWriteCmd", {
+    buffer = bufnr,
+    once = true,
+    callback = function()
+      on_write()
+      vim.cmd("bd! " .. bufnr)
+    end
+  })
+
+  vim.cmd("split")
+  vim.cmd("buffer " .. bufnr)
+
+  vim.wait(60000, function()
+    local winids = vim.api.nvim_tabpage_list_wins(0)
+    for _, w in ipairs(winids) do
+      local b = vim.api.nvim_win_get_buf(w)
+      if b == bufnr then
+        return false
+      end
+    end
+    return true
+  end)
+
+  return final_changes
+end
+
+local function store_prompt_for_reference(prompt, conf)
+  close_existing_buffer_by_name("ChatGPT_Generated_Prompt$")
+  local bufnr = vim.api.nvim_create_buf(false, true)
+  vim.api.nvim_buf_set_name(bufnr, "ChatGPT_Generated_Prompt")
+  vim.api.nvim_buf_set_option(bufnr, "filetype", "markdown")
+
+  local lines = {
+    "# Below is the generated prompt. You can keep it for reference:",
+    ""
+  }
+  local prompt_lines = vim.split(prompt, "\n")
+  for _, line in ipairs(prompt_lines) do
+    table.insert(lines, line)
+  end
+
+  vim.api.nvim_buf_set_lines(bufnr, 0, -1, false, lines)
+  vim.cmd("vsplit")
+  vim.cmd("buffer " .. bufnr)
+end
+
+-- Updated to allow flags/args for 'ls' and 'grep'
+local function execute_debug_command(cmd, conf)
+  if type(cmd) ~= "table" or not cmd.command then
+    return "Invalid command object."
+  end
+
+  local command = cmd.command
+  if command == "ls" then
+    -- Accept optional flags/args
+    local dir = cmd.dir or "."
+    local args = cmd.args or {}
+    local cmd_str = "ls"
+    if #args > 0 then
+      cmd_str = cmd_str .. " " .. table.concat(args, " ")
+    end
+    cmd_str = cmd_str .. " " .. dir
+
+    local handle = io.popen(cmd_str)
+    if not handle then
+      return "Failed to run ls command."
+    end
+    local result = handle:read("*a") or ""
+    handle:close()
+    return "Listing files in: " .. dir .. "\n" .. result
+
+  elseif command == "grep" then
+    -- Accept optional flags/args
+    -- If the user wants to do something like:
+    --   args: ["-r", "somePattern", "someDir"]
+    -- we just pass them all to grep.
+    local args = cmd.args or {}
+    if #args == 0 then
+      -- fallback to old usage
+      local pattern = cmd.pattern
+      local target = cmd.target
+      if not pattern or not target then
+        return "Usage for grep: {command='grep', args=['-r','pattern','target']} or {pattern='<text>', target='<path>'}"
+      end
+      local stat = vim.loop.fs_stat(target)
+      if not stat then
+        return "Cannot grep: target path does not exist"
+      end
+      -- old logic remains for backward compatibility
+      if stat.type == "directory" then
+        local handle = io.popen("ls -p " .. target .. " | grep -v /")
+        if not handle then
+          return "Failed to read directory contents for grep."
+        end
+        local all_files = {}
+        for file in handle:read("*a"):gmatch("[^\n]+") do
+          table.insert(all_files, target .. "/" .. file)
+        end
+        handle:close()
+        local results = {}
+        local function grep_in_file(search_string, filepath)
+          local content = read_file(filepath)
+          if not content then
+            return "Could not read file: " .. filepath
+          end
+          local lines = {}
+          local line_num = 0
+          for line in content:gmatch("([^\n]*)\n?") do
+            line_num = line_num + 1
+            if line:find(search_string, 1, true) then
+              table.insert(lines, filepath .. ":" .. line_num .. ":" .. line)
+            end
+          end
+          return (#lines == 0) and ("No matches in " .. filepath) or table.concat(lines, "\n")
+        end
+        for _, f in ipairs(all_files) do
+          local fstat = vim.loop.fs_stat(f)
+          if fstat and fstat.type == "file" then
+            table.insert(results, grep_in_file(pattern, f))
+          end
+        end
+        return table.concat(results, "\n")
+      else
+        local function grep_in_file(search_string, filepath)
+          local content = read_file(filepath)
+          if not content then
+            return "Could not read file: " .. filepath
+          end
+          local lines = {}
+          local line_num = 0
+          for line in content:gmatch("([^\n]*)\n?") do
+            line_num = line_num + 1
+            if line:find(search_string, 1, true) then
+              table.insert(lines, filepath .. ":" .. line_num .. ":" .. line)
+            end
+          end
+          return (#lines == 0) and ("No matches in " .. filepath) or table.concat(lines, "\n")
+        end
+        return grep_in_file(pattern, target)
+      end
+    else
+      -- new approach with flags/args
+      local cmd_str = "grep " .. table.concat(args, " ")
+      local handle = io.popen(cmd_str)
+      if not handle then
+        return "Failed to run grep command."
+      end
+      local result = handle:read("*a") or ""
+      handle:close()
+      return result
+    end
+  else
+    return "Unknown command: " .. command
   end
-  return { prompts["step-prompt"] }
 end
 
-------------------------------------------------------------------------------
--- :ChatGPT
-------------------------------------------------------------------------------
 local function run_chatgpt_command()
   local conf = config.load()
   ui.setup_ui(conf)
@@ -176,7 +350,7 @@ local function run_chatgpt_command()
   vim.api.nvim_buf_set_option(bufnr, "modifiable", true)
 
   vim.api.nvim_buf_set_lines(bufnr, 0, -1, false, {
-    "# Enter your main user prompt (task) below.",
+    "# Enter your prompt below.",
     "",
     "Save & close with :wq, :x, or :bd to finalize your prompt."
   })
@@ -186,25 +360,57 @@ local function run_chatgpt_command()
     callback = function()
       local lines = vim.api.nvim_buf_get_lines(bufnr, 0, -1, false)
       local user_input = table.concat(lines, "\n")
-      if user_input == "" or user_input:find("^# Enter your main user prompt %(task%) below.") then
+      if user_input == "" or user_input:find("^# Enter your prompt below.") then
         vim.api.nvim_out_write("No valid input provided.\n")
         vim.api.nvim_buf_set_option(bufnr, "modified", false)
         return
       end
 
-      local final_prompt = build_prompt(user_input, dirs, conf)
-      local chunks = handle_step_by_step_if_needed(final_prompt, conf)
+      local project_structure = context.get_project_structure(dirs, conf)
+      local initial_files = conf.initial_files or {}
+      local included_sections = {}
 
-      close_existing_buffer_by_name("ChatGPT_Generated_Prompt$")
-      local bufnr_ref = vim.api.nvim_create_buf(false, true)
-      vim.api.nvim_buf_set_name(bufnr_ref, "ChatGPT_Generated_Prompt")
-      vim.api.nvim_buf_set_option(bufnr_ref, "filetype", "markdown")
+      for _, item in ipairs(initial_files) do
+        local root = vim.fn.getcwd()
+        local full_path = root .. "/" .. item
+        if is_directory(full_path) then
+          local dir_files = context.get_project_files({item}, conf)
+          for _, f in ipairs(dir_files) do
+            local path = root .. "/" .. f
+            local data = read_file(path)
+            if data then
+              table.insert(included_sections, "\nFile: `" .. f .. "`\n```\n" .. data .. "\n```\n")
+            end
+          end
+        else
+          local data = read_file(full_path)
+          if data then
+            table.insert(included_sections, "\nFile: `" .. item .. "`\n```\n" .. data .. "\n```\n")
+          end
+        end
+      end
 
-      local prompt_lines = vim.split(chunks[1], "\n")
-      vim.api.nvim_buf_set_lines(bufnr_ref, 0, -1, false, prompt_lines)
-      vim.cmd("vsplit")
-      vim.cmd("buffer " .. bufnr_ref)
+      local initial_sections = {
+        "## Basic Prompt Instructions:\n",
+        conf.initial_prompt .. "\n\n\n",
+        "## User Instructions:\n",
+        user_input .. "\n\n\n",
+        "## Context/Data:\n",
+        "Project name: " .. (conf.project_name or "") .. "\n",
+        "Project Structure:\n",
+        project_structure,
+        table.concat(included_sections, "\n")
+      }
 
+      if conf.enable_debug_commands then
+        table.insert(initial_sections, "\n## Debug Commands Info:\n")
+        table.insert(initial_sections, prompts["debug-commands-info"])
+      end
+
+      local prompt = table.concat(initial_sections, "\n")
+      store_prompt_for_reference(prompt, conf)
+
+      local chunks = handle_step_by_step_if_needed(prompt, conf)
       copy_to_clipboard(chunks[1])
       if #chunks == 1 then
         vim.api.nvim_out_write("Prompt copied to clipboard! Paste into ChatGPT.\n")
@@ -219,9 +425,6 @@ local function run_chatgpt_command()
   vim.cmd("buffer " .. bufnr)
 end
 
-------------------------------------------------------------------------------
--- :ChatGPTPaste
-------------------------------------------------------------------------------
 local function run_chatgpt_paste_command()
   local conf = config.load()
   ui.setup_ui(conf)
@@ -238,22 +441,19 @@ local function run_chatgpt_paste_command()
     return
   end
 
-  -- Check if we have tools
-  if data.tools then
-    -- Must also verify project name
-    if not data.project_name or data.project_name ~= conf.project_name then
-      vim.api.nvim_err_writeln("Project name mismatch or missing. Aborting tool usage.")
-      return
+  if data.commands and conf.enable_debug_commands then
+    local results = {}
+    for _, cmd in ipairs(data.commands) do
+      table.insert(results, execute_debug_command(cmd, conf))
     end
-
-    local output_messages = tools_manager.handle_tool_calls(data.tools, conf, is_subpath, read_file)
-    copy_to_clipboard(output_messages)
-    print("Tool call results have been processed and copied to clipboard.")
+    local output = table.concat(results, "\n\n")
+    copy_to_clipboard(output)
+    print("Debug command results copied to clipboard!")
     return
   end
 
-  -- If we see project_name & files => older YAML style. We handle it but it's discouraged now.
   if data.project_name and data.files then
+    ui.debug_log("Received project_name and files in response.")
     if data.project_name ~= conf.project_name then
       vim.api.nvim_err_writeln("Project name mismatch. Aborting.")
       return
@@ -269,7 +469,7 @@ local function run_chatgpt_paste_command()
 
     if is_final then
       if conf.preview_changes then
-        require('chatgpt_nvim.init').preview_changes(data.files, conf)
+        preview_changes(data.files, conf)
         print("Close the preview window to apply changes, or use :q to cancel.")
         local closed = vim.wait(60000, function()
           local bufs = vim.api.nvim_list_bufs()
@@ -289,7 +489,7 @@ local function run_chatgpt_paste_command()
 
       local final_files = data.files
       if conf.partial_acceptance then
-        final_files = require('chatgpt_nvim.init').partial_accept(data.files, conf)
+        final_files = partial_accept(data.files, conf)
         if #final_files == 0 then
           vim.api.nvim_err_writeln("No changes remain after partial acceptance. Aborting.")
           return
@@ -300,28 +500,30 @@ local function run_chatgpt_paste_command()
       for _, fileinfo in ipairs(final_files) do
         if not fileinfo.path then
           vim.api.nvim_err_writeln("Invalid file entry. Must have 'path'.")
-        else
-          if not is_subpath(root, fileinfo.path) then
-            vim.api.nvim_err_writeln("Invalid path outside project root: " .. fileinfo.path)
-          else
-            if fileinfo.delete == true then
-              ui.debug_log("Deleting file: " .. fileinfo.path)
-              handler.delete_file(fileinfo.path, conf)
-              print("Deleted: " .. fileinfo.path)
-            elseif fileinfo.content then
-              ui.debug_log("Writing file: " .. fileinfo.path)
-              handler.write_file(fileinfo.path, fileinfo.content, conf)
-              print("Wrote: " .. fileinfo.path)
-            else
-              vim.api.nvim_err_writeln("Invalid file entry. Must have 'content' or 'delete'.")
-            end
-          end
+          goto continue
         end
+
+        if not is_subpath(root, fileinfo.path) then
+          vim.api.nvim_err_writeln("Invalid path outside project root: " .. fileinfo.path)
+          goto continue
+        end
+
+        if fileinfo.delete == true then
+          ui.debug_log("Deleting file: " .. fileinfo.path)
+          handler.delete_file(fileinfo.path, conf)
+          print("Deleted: " .. fileinfo.path)
+        elseif fileinfo.content then
+          ui.debug_log("Writing file: " .. fileinfo.path)
+          handler.write_file(fileinfo.path, fileinfo.content, conf)
+          print("Wrote: " .. fileinfo.path)
+        else
+          vim.api.nvim_err_writeln("Invalid file entry. Must have 'content' or 'delete'.")
+        end
+        ::continue::
       end
+
     else
-      -- Not final => user is requesting more files
       local requested_paths = {}
-      local root = vim.fn.getcwd()
       for _, fileinfo in ipairs(data.files) do
         if fileinfo.path then
           table.insert(requested_paths, fileinfo.path)
@@ -329,13 +531,14 @@ local function run_chatgpt_paste_command()
       end
 
       local file_sections = {}
+      local root = vim.fn.getcwd()
       for _, f in ipairs(requested_paths) do
         local path = root .. "/" .. f
         local content = read_file(path)
         if content then
-          table.insert(file_sections, ("\nFile: `%s`\n```\n%s\n```\n"):format(f, content))
+          table.insert(file_sections, "\nFile: `" .. f .. "`\n```\n" .. content .. "\n```\n")
         else
-          table.insert(file_sections, ("\nFile: `%s`\n```\n(Could not read file)\n```\n"):format(f))
+          table.insert(file_sections, "\nFile: `" .. f .. "`\n```\n(Could not read file)\n```\n")
         end
       end
 
@@ -344,7 +547,7 @@ local function run_chatgpt_paste_command()
         "\n\nProject name: " .. (conf.project_name or ""),
         "\n\nBelow are the requested files from the project, each preceded by its filename in backticks and enclosed in triple backticks.\n",
         table.concat(file_sections, "\n"),
-        "\n\nIf you need more files, please respond again in YAML listing additional files, or use the 'tools:' approach. If you have all info, provide final changes or continue your instructions."
+        "\n\nIf you need more files, please respond again in YAML listing additional files. If you have all information you need, provide the final YAML with `project_name` and `files` (with `content` or `delete`) to apply changes.\n"
       }
 
       local prompt = table.concat(sections, "\n")
@@ -362,21 +565,17 @@ local function run_chatgpt_paste_command()
       end
 
       copy_to_clipboard(prompt)
-      print("Prompt (with requested files) copied to clipboard! Paste it into ChatGPT.")
+      print("Prompt (with requested files) copied to clipboard! Paste it into the ChatGPT O1 model.")
     end
   else
-    vim.api.nvim_err_writeln("No tools or recognized file instructions found. Provide 'tools:' or older 'project_name & files'.")
+    vim.api.nvim_err_writeln("Invalid response. Expected 'project_name' and 'files'.")
   end
 end
 
-------------------------------------------------------------------------------
--- :ChatGPTCurrentBuffer
-------------------------------------------------------------------------------
 local function run_chatgpt_current_buffer_command()
   local conf = config.load()
   ui.setup_ui(conf)
   ui.debug_log("Running :ChatGPTCurrentBuffer command.")
-
   local lines = vim.api.nvim_buf_get_lines(0, 0, -1, false)
   local user_input = table.concat(lines, "\n")
   local dirs = conf.directories or {"."}
@@ -387,19 +586,92 @@ local function run_chatgpt_current_buffer_command()
     end
   end
 
-  local final_prompt = build_prompt(user_input, dirs, conf)
-  local chunks = handle_step_by_step_if_needed(final_prompt, conf)
+  local project_structure = context.get_project_structure(dirs, conf)
+  local initial_files = conf.initial_files or {}
+  local included_sections = {}
 
-  close_existing_buffer_by_name("ChatGPT_Generated_Prompt$")
-  local bufnr_ref = vim.api.nvim_create_buf(false, true)
-  vim.api.nvim_buf_set_name(bufnr_ref, "ChatGPT_Generated_Prompt")
-  vim.api.nvim_buf_set_option(bufnr_ref, "filetype", "markdown")
+  local function is_directory(path)
+    local stat = vim.loop.fs_stat(path)
+    return stat and stat.type == "directory"
+  end
 
-  local prompt_lines = vim.split(chunks[1], "\n")
-  vim.api.nvim_buf_set_lines(bufnr_ref, 0, -1, false, prompt_lines)
-  vim.cmd("vsplit")
-  vim.cmd("buffer " .. bufnr_ref)
+  local function read_file(path)
+    local fd = vim.loop.fs_open(path, "r", 438)
+    if not fd then
+      return nil
+    end
+    local stat = vim.loop.fs_fstat(fd)
+    if not stat then
+      vim.loop.fs_close(fd)
+      return nil
+    end
+    local data = vim.loop.fs_read(fd, stat.size, 0)
+    vim.loop.fs_close(fd)
+    return data
+  end
 
+  for _, item in ipairs(initial_files) do
+    local root = vim.fn.getcwd()
+    local full_path = root .. "/" .. item
+    if is_directory(full_path) then
+      local dir_files = context.get_project_files({item}, conf)
+      for _, f in ipairs(dir_files) do
+        local path = root .. "/" .. f
+        local data = read_file(path)
+        if data then
+          table.insert(included_sections, "\nFile: `" .. f .. "`\n```\n" .. data .. "\n```\n")
+        end
+      end
+    else
+      local data = read_file(full_path)
+      if data then
+        table.insert(included_sections, "\nFile: `" .. item .. "`\n```\n" .. data .. "\n```\n")
+      end
+    end
+  end
+
+  local initial_sections = {
+    "## Basic Prompt Instructions:\n",
+    conf.initial_prompt .. "\n\n\n",
+    "## User Instructions:\n",
+    user_input .. "\n\n\n",
+    "## Context/Data:\n",
+    "Project name: " .. (conf.project_name or "") .. "\n",
+    "Project Structure:\n",
+    project_structure,
+    table.concat(included_sections, "\n")
+  }
+
+  if conf.enable_debug_commands then
+    table.insert(initial_sections, "\n## Debug Commands Info:\n")
+    table.insert(initial_sections, prompts["debug-commands-info"])
+  end
+
+  local prompt = table.concat(initial_sections, "\n")
+
+  local function store_prompt_for_reference(pr)
+    close_existing_buffer_by_name("ChatGPT_Generated_Prompt$")
+    local bufnr_ref = vim.api.nvim_create_buf(false, true)
+    vim.api.nvim_buf_set_name(bufnr_ref, "ChatGPT_Generated_Prompt")
+    vim.api.nvim_buf_set_option(bufnr_ref, "filetype", "markdown")
+
+    local lines_ref = {
+      "# Below is the generated prompt. You can keep it for reference:",
+      ""
+    }
+    local pr_lines = vim.split(pr, "\n")
+    for _, line in ipairs(pr_lines) do
+      table.insert(lines_ref, line)
+    end
+
+    vim.api.nvim_buf_set_lines(bufnr_ref, 0, -1, false, lines_ref)
+    vim.cmd("vsplit")
+    vim.cmd("buffer " .. bufnr_ref)
+  end
+
+  store_prompt_for_reference(prompt, conf)
+
+  local chunks = handle_step_by_step_if_needed(prompt, conf)
   copy_to_clipboard(chunks[1])
   if #chunks == 1 then
     vim.api.nvim_out_write("Prompt (from current buffer) copied to clipboard! Paste into ChatGPT.\n")
@@ -408,11 +680,9 @@ local function run_chatgpt_current_buffer_command()
   end
 end
 
-------------------------------------------------------------------------------
--- PUBLIC API
-------------------------------------------------------------------------------
 M.run_chatgpt_command = run_chatgpt_command
 M.run_chatgpt_paste_command = run_chatgpt_paste_command
 M.run_chatgpt_current_buffer_command = run_chatgpt_current_buffer_command
+M.execute_debug_command = execute_debug_command
 
 return M
diff --git a/lua/chatgpt_nvim/prompts.lua b/lua/chatgpt_nvim/prompts.lua
index 941ddab..9e00cd5 100644
--- a/lua/chatgpt_nvim/prompts.lua
+++ b/lua/chatgpt_nvim/prompts.lua
@@ -44,7 +44,7 @@ local M = {
     5. **Styling & CSS Management**  
        - Use your preferred styling approach (CSS Modules, [Tailwind CSS](https://tailwindcss.com/), or standard CSS/SCSS files).  
        - Keep global styles minimal, focusing on utility classes or base styling; keep component-level styles scoped whenever possible.  
-     - If using CSS-in-JS solutions or third-party libraries, ensure they integrate cleanly with Solid’s reactivity.  
+       - If using CSS-in-JS solutions or third-party libraries, ensure they integrate cleanly with Solid’s reactivity.  
 
     6. **TypeScript & Linting**  
        - Use **TypeScript** to ensure type safety and improve maintainability.  
@@ -81,7 +81,7 @@ local M = {
     1. **Go Modules**  
        - Use a single `go.mod` file at the project root for module management.  
        - Ensure you use proper import paths based on the module name.  
-     - If you refer to internal packages, use relative paths consistent with the module’s structure (e.g., `moduleName/internal/packageA`).  
+       - If you refer to internal packages, use relative paths consistent with the module’s structure (e.g., `moduleName/internal/packageA`).  
 
     2. **Package Structure**  
        - Each folder should contain exactly one package.  
@@ -110,21 +110,21 @@ local M = {
     4. **Coding Best Practices**  
        - Maintain idiomatic Go code (e.g., short function and variable names where obvious, PascalCase for exported symbols).  
        - Keep functions short, focused, and tested.  
-     - Use Go’s standard library where possible before adding third-party dependencies.  
+       - Use Go’s standard library where possible before adding third-party dependencies.  
        - When introducing new functions or types, ensure they are uniquely named to avoid collisions.  
 
     5. **Import Management**  
        - Ensure that every import is actually used in your code.  
        - Remove unused imports to keep your code clean and maintainable.  
        - Include all necessary imports for anything referenced in your code to avoid missing imports.  
-     - Verify that any introduced import paths match your module’s structure and do not cause naming conflicts.  
+       - Verify that any introduced import paths match your module’s structure and do not cause naming conflicts.  
 
     6. **Output Format**  
        - Present any generated source code as well-organized Go files, respecting the single-package-per-folder rule.  
        - When explaining your reasoning, include any relevant architectural trade-offs and rationale (e.g., “I placed function X in package Y to keep the domain-specific logic separate from the main execution flow.”).  
        - If you modify an existing file, specify precisely which changes or additions you are making.  
 
-  Please follow these guidelines to ensure the generated or explained code aligns well with Golang’s best practices for large, modular projects.
+    Please follow these guidelines to ensure the generated or explained code aligns well with Golang’s best practices for large, modular projects.
   ]],
   ["typo3-development"] = [[
     ### TYPO3 Development Guidelines
@@ -150,10 +150,10 @@ local M = {
        - Keep site configuration in `config/sites/` (for TYPO3 v9+).  
 
     2. **Extension Development**  
-     - Create custom functionality as separate extensions (site packages, domain-specific extensions, etc.) following TYPO3’s recommended structure:
+       - Create custom functionality as separate extensions (site packages, domain-specific extensions, etc.) following TYPO3’s recommended structure:
          - **Key files**: `ext_emconf.php`, `ext_localconf.php`, `ext_tables.php`, `ext_tables.sql`, `Configuration/`, `Classes/`, `Resources/`.  
          - Use **PSR-4** autoloading and name extensions logically (e.g., `my_sitepackage`, `my_blogextension`).  
-     - Keep your extension’s code under `Classes/` (e.g., Controllers, Models, Services).  
+       - Keep your extension’s code under `Classes/` (e.g., Controllers, Models, Services).  
        - Place Fluid templates, partials, and layouts under `Resources/Private/` (e.g., `Resources/Private/Templates`, `Resources/Private/Partials`, `Resources/Private/Layouts`).  
 
     3. **Configuration (TypoScript & TCA)**  
@@ -186,10 +186,10 @@ local M = {
     7. **Output Format**  
        - Present any generated source code or configuration files in a well-organized structure.  
        - Clearly indicate where each file should be placed in the TYPO3 directory layout.  
-     - When explaining your reasoning, include any relevant architectural decisions (e.g., “I created a separate extension for blog functionality to keep it isolated from the site’s main configuration.”).  
+       - When explaining your reasoning, include any relevant architectural decisions (e.g., “I created a separate extension for blog functionality to keep it isolated from the site’s main configuration.”).  
        - If you modify or extend an existing file, specify precisely which changes or additions you are making.  
 
-  Please follow these guidelines to ensure the generated or explained code aligns well with TYPO3’s best practices for large, maintainable projects.
+    Please follow these guidelines to ensure the generated or explained code aligns well with TYPO3’s best practices for large, maintainable projects.
   ]],
   ["rust-development"] = [[
     ### Rust Development Guidelines
@@ -204,11 +204,11 @@ local M = {
     2. **Crates & Packages**  
        - Split the application into logical crates (libraries and/or binaries).  
        - Each crate should have a single main **library** (`lib.rs`) or **binary** (`main.rs`) in its `src/` folder.  
-     - Name crates, modules, and files clearly, following Rust’s naming conventions (e.g., `snake_case` for files/modules, `PascalCase` for types).  
+       - Name crates, modules, and files clearly, following Rust’s naming conventions (e.g., `snake_case` for files/modules, `PascalCase` for types).  
        - Avoid duplicating the same function or type in multiple crates; share common functionality via a dedicated library crate if needed.  
 
     3. **Folder & Module Structure**  
-     - Organize code within each crate using Rust’s module system, keeping related functions and types in logical modules/submodules.  
+       - Organize code within each crate using Rust’s module system, keeping related functions and types in logical modules/submodules.  
        - A typical directory layout for a workspace with multiple crates might look like:
          ```
          myproject/
@@ -226,7 +226,7 @@ local M = {
          ├── target/
          └── ...
          ```
-     - If you have integration tests, store them in a `tests/` folder at the crate root, or use the workspace root’s `tests/` directory if they span multiple crates.  
+       - If you have integration tests, store them in a `tests/` folder at the crate root, or use the workspace root’s `tests/` directory if they span multiple crates.  
 
     4. **Coding & Documentation Best Practices**  
        - Write **idiomatic Rust** code:
@@ -256,41 +256,54 @@ local M = {
   ["basic-prompt"] = [[
     ### Basic Prompt
 
-    You are assisting me in a coding workflow for a project (e.g., "my_project"). Whenever you need to inspect or modify files, or execute commands, you must provide both:
+    1. **Analyze Required Files**  
+       - Check the project structure (or any provided file list).
+       - If you identify a file reference or function you do not have, **produce a YAML snippet** requesting that file’s content in full. For example:
+         ```yaml
+         project_name: my_project
+         files:
+           - path: "relative/path/to/needed_file"
+         ```
+       - Do not proceed with final changes if you lack the necessary file contents.
+       - Always provide the entire file content when you do include a file.
 
-    1. `project_name: "<actual_project_name>"` (matching the real project name)  
-    2. A `tools:` array describing the operations you want to perform.
+    2. **Request File Contents**  
+       - For every file you need but don’t have, provide a short YAML snippet (like above) to retrieve it.
+       - Ask any clarifying questions outside the YAML code block.
 
-    **Example** (substitute `<actual_project_name>` with the real name):
-    ```yaml
-    project_name: "my_project"
-    tools:
-      - tool: "readFile"
-        path: "relative/path/to/file"
+    3. **Provide Output YAML**  
+       - When you have all information, output the final YAML in this format:
+         ```yaml
+         project_name: my_project
 
-      - tool: "replace_in_file"
-        path: "relative/path/to/file"
-        replacements:
-          - search: "old text"
-            replace: "new text"
+         files:
+           - path: "src/main.py"
+             content: |
+               # Updated main function
+               def main():
+                   print("Hello, World!")
 
-      - tool: "editFile"
-        path: "relative/path/to/file"
-        content: |
-          # Full updated file content here
+           - path: "docs/README.md"
+             delete: true
+         ```
+       - `project_name` must match the project’s configured name.
+       - Each file item in `files` must have `path` and either `content` or `delete: true`.
 
-      - tool: "executeCommand"
-        command: "ls -la"
-    ```
+    4. **Explain Changes**  
+       - After the final YAML, add a brief explanation of the modifications (outside the YAML).
 
-    **Key Points**:
-    - Always include `project_name: "<actual_project_name>"` in the same YAML as `tools`.
-    - If you only need one tool, include just one object in the `tools` array.
-    - If multiple tools are needed, list them sequentially in the `tools` array.
-    - Always run at least one tool (e.g., `readFile`, `editFile`, `executeCommand`), exept you have finished.
-    - Always just include one yaml in the response with all the tools you want to run in that yaml.
-    - The plugin will verify the `project_name` is correct before running any tools.
-    - If the response grows too large, I'll guide you to break it into smaller steps.
+    5. **Iterate as Needed**  
+       - If further context or changes are required, repeat steps to request files or clarifications.
+
+    6. **Important Notes**  
+       - Never modify or delete a file you haven’t explicitly requested or received.
+       - Use comments in code only to clarify code logic, not to explain your thought process.
+       - Explanations go outside the YAML.
+
+    7. **Best Practices**  
+       - Keep file paths accurate to avoid mistakes during implementation.
+       - Maintain a clear, logical structure for your changes.
+       - Use the final YAML consistently for clarity.
   ]],
   ["secure-coding"] = [[
     ### Secure Coding Guidelines
@@ -357,10 +370,33 @@ local M = {
   ["step-prompt"] = [[
     It appears this request might exceed the model's prompt character limit if done all at once.
     Please break down the tasks into smaller steps and handle them one by one.
+    At each step, we'll provide relevant files or context if needed.
     Thank you!
   ]],
   ["file-selection-instructions"] = [[
     Delete lines for directories you do NOT want, then save & close (e.g. :wq, :x, or :bd)
+  ]],
+  ["debug-commands-info"] = [[
+    ### Debugging Commands
+
+    If you need debugging commands, include them in your YAML response as follows:
+
+    ```yaml
+    commands:
+      - command: "ls"
+        args: ["-l", "path/to/directory"]
+
+      - command: "grep"
+        args: ["-r", "searchString", "path/to/file/or/directory"]
+    ```
+
+    The "ls" command uses the system's 'ls' command to list directory contents. You can pass flags or additional arguments in `args`.
+    The "grep" command searches for a given pattern in files or directories, again receiving flags or additional arguments in `args`.
+    If you omit `args` for grep, you can still use the older format with `pattern` and `target` for backward compatibility.
+
+    This are the only two commands supported at the moment.
+
+    When these commands are present and `enable_debug_commands` is true, I'll execute them and return the results in the clipboard.
   ]]
 }
 
diff --git a/lua/chatgpt_nvim/tools/edit_file.lua b/lua/chatgpt_nvim/tools/edit_file.lua
deleted file mode 100644
index 35fdb3f..0000000
--- a/lua/chatgpt_nvim/tools/edit_file.lua
+++ /dev/null
@@ -1,37 +0,0 @@
-local handler = require("chatgpt_nvim.handler")
-local robust_lsp = require("chatgpt_nvim.tools.lsp_robust_diagnostics")
-
-local M = {}
-
-M.run = function(tool_call, conf, prompt_user_tool_accept, is_subpath, read_file)
-  local path = tool_call.path
-  local new_content = tool_call.content
-
-  if not path or not new_content then
-    return "[edit_file] Missing 'path' or 'content'."
-  end
-  local root = vim.fn.getcwd()
-
-  if not is_subpath(root, path) then
-    return string.format("Tool [edit_file for '%s'] REJECTED. Path outside project root.", path)
-  end
-
-  -- 1) Write the new content
-  handler.write_file(path, new_content, conf)
-
-  local msg = {}
-  msg[#msg+1] = string.format("Tool [edit_file for '%s'] Result:\nThe content was successfully saved to %s.", path, path)
-  msg[#msg+1] = "\nHere is the full, updated content of the file that was saved:\n"
-  msg[#msg+1] = string.format("<final_file_content path=\"%s\">\n%s\n</final_file_content>", path, new_content)
-  msg[#msg+1] = "\nIMPORTANT: For any future changes to this file, use the final_file_content shown above as your reference.\n"
-
-  -- 2) If auto_lint => run robust LSP approach
-  if conf.auto_lint then
-    local diag_str = robust_lsp.lsp_check_file_content(path, new_content, 3000) -- 3s wait
-    msg[#msg+1] = "\n" .. diag_str
-  end
-
-  return table.concat(msg, "")
-end
-
-return M
diff --git a/lua/chatgpt_nvim/tools/execute_command.lua b/lua/chatgpt_nvim/tools/execute_command.lua
deleted file mode 100644
index 5fb9274..0000000
--- a/lua/chatgpt_nvim/tools/execute_command.lua
+++ /dev/null
@@ -1,17 +0,0 @@
-local M = {}
-
-M.run = function(tool_call, conf, prompt_user_tool_accept, is_subpath, read_file)
-  local cmd = tool_call.command
-  if not cmd then
-    return "[executeCommand] Missing 'command'."
-  end
-  local handle = io.popen(cmd)
-  if not handle then
-    return string.format("Tool [executeCommand '%s'] FAILED to popen.", cmd)
-  end
-  local result = handle:read("*a") or ""
-  handle:close()
-  return string.format("Tool [executeCommand '%s'] Result:\n%s", cmd, result)
-end
-
-return M
diff --git a/lua/chatgpt_nvim/tools/init.lua b/lua/chatgpt_nvim/tools/init.lua
deleted file mode 100644
index 48383dd..0000000
--- a/lua/chatgpt_nvim/tools/init.lua
+++ /dev/null
@@ -1,39 +0,0 @@
-local read_file_tool = require("chatgpt_nvim.tools.read_file")
-local edit_file_tool = require("chatgpt_nvim.tools.edit_file")
-local replace_in_file_tool = require("chatgpt_nvim.tools.replace_in_file")
-local execute_command_tool = require("chatgpt_nvim.tools.execute_command")
-
-local M = {}
-
--- We can store a table of available tools here
-M.available_tools = {
-  {
-    name = "readFile",
-    usage = "Retrieve the contents of a file. Provide { tool='readFile', path='...' }",
-    explanation = "Use this to read file content directly from the disk."
-  },
-  {
-    name = "editFile",
-    usage = "Overwrite an entire file's content. Provide { tool='editFile', path='...', content='...' }",
-    explanation = "Use this when you want to replace a file with new content."
-  },
-  {
-    name = "replace_in_file",
-    usage = "Perform a search-and-replace. Provide { tool='replace_in_file', path='...', replacements=[ { search='...', replace='...' }, ... ] }",
-    explanation = "Use this to apply incremental changes without fully overwriting the file."
-  },
-  {
-    name = "executeCommand",
-    usage = "Run a shell command. Provide { tool='executeCommand', command='...' }",
-    explanation = "Use with caution, especially for destructive operations (rm, sudo, etc.)."
-  },
-}
-
-M.tools_by_name = {
-  readFile = read_file_tool,
-  editFile = edit_file_tool,
-  replace_in_file = replace_in_file_tool,
-  executeCommand = execute_command_tool
-}
-
-return M
diff --git a/lua/chatgpt_nvim/tools/lsp_robust_diagnostics.lua b/lua/chatgpt_nvim/tools/lsp_robust_diagnostics.lua
deleted file mode 100644
index 8693c2b..0000000
--- a/lua/chatgpt_nvim/tools/lsp_robust_diagnostics.lua
+++ /dev/null
@@ -1,177 +0,0 @@
-local api = vim.api
-local lsp = vim.lsp
-
-local M = {}
-
-local function guess_filetype(path)
-  local ext = path:match("^.+%.([^./\\]+)$")
-  if not ext then return nil end
-  ext = ext:lower()
-  local map = {
-    lua = "lua",
-    go  = "go",
-    rs  = "rust",
-    js  = "javascript",
-    jsx = "javascriptreact",
-    ts  = "typescript",
-    tsx = "typescriptreact",
-    php = "php",
-  }
-  return map[ext]
-end
-
-local function create_scratch_buffer(path, content)
-  -- Create a unique buffer name so we never clash with an existing one
-  local scratch_name = string.format("chatgpt-scratch://%s#%d", path, math.random(100000, 999999))
-
-  local bufnr = api.nvim_create_buf(false, true)
-  if bufnr == 0 then
-    return nil
-  end
-
-  -- Assign the unique name to the buffer
-  api.nvim_buf_set_name(bufnr, scratch_name)
-
-  -- Convert content string to lines
-  local lines = {}
-  for line in (content.."\n"):gmatch("(.-)\n") do
-    table.insert(lines, line)
-  end
-  api.nvim_buf_set_lines(bufnr, 0, -1, false, lines)
-
-  -- Mark it as a scratch buffer
-  api.nvim_buf_set_option(bufnr, "bufhidden", "wipe")
-  api.nvim_buf_set_option(bufnr, "swapfile", false)
-
-  return bufnr
-end
-
-local function attach_existing_lsp_client(bufnr, filetype)
-  local clients = lsp.get_active_clients()
-  if not clients or #clients == 0 then
-    return nil, "No active LSP clients"
-  end
-
-  for _, client in ipairs(clients) do
-    local ft_conf = client.config.filetypes or {}
-    if vim.tbl_contains(ft_conf, filetype) then
-      if not client.attached_buffers[bufnr] then
-        vim.lsp.buf_attach_client(bufnr, client.id)
-      end
-      return client.id
-    end
-  end
-  return nil, ("No active LSP client supports filetype '%s'"):format(filetype)
-end
-
-local function send_did_open(bufnr, client_id, path, filetype)
-  local client = lsp.get_client_by_id(client_id)
-  if not client then
-    return "Invalid client ID."
-  end
-
-  local text = table.concat(api.nvim_buf_get_lines(bufnr, 0, -1, false), "\n")
-  -- Even though the buffer name is unique, the LSP server sees this file as if at 'path'
-  local uri = vim.uri_from_fname(path)
-
-  local didOpenParams = {
-    textDocument = {
-      uri = uri,
-      languageId = filetype,
-      version = 0,
-      text = text,
-    }
-  }
-  client.rpc.notify("textDocument/didOpen", didOpenParams)
-  return nil
-end
-
-local function send_did_change(bufnr, client_id)
-  local client = lsp.get_client_by_id(client_id)
-  if not client then return end
-
-  local text = table.concat(api.nvim_buf_get_lines(bufnr, 0, -1, false), "\n")
-  local uri = vim.uri_from_bufnr(bufnr)
-  local version = 1
-
-  client.rpc.notify("textDocument/didChange", {
-    textDocument = {
-      uri = uri,
-      version = version,
-    },
-    contentChanges = {
-      { text = text }
-    }
-  })
-end
-
-local function wait_for_diagnostics(bufnr, timeout_ms)
-  local done = false
-  local result_diags = {}
-
-  local augrp = api.nvim_create_augroup("chatgpt_lsp_diag_"..bufnr, { clear = true })
-  api.nvim_create_autocmd("DiagnosticChanged", {
-    group = augrp,
-    callback = function(args)
-      if args.buf == bufnr then
-        local diags = vim.diagnostic.get(bufnr)
-        result_diags = diags
-        done = true
-      end
-    end
-  })
-
-  local waited = 0
-  local interval = 50
-  while not done and waited < timeout_ms do
-    vim.cmd(("sleep %d m"):format(interval))
-    waited = waited + interval
-  end
-
-  pcall(api.nvim_del_augroup_by_id, augrp)
-  return result_diags
-end
-
-local function diagnostics_to_string(diags)
-  if #diags == 0 then
-    return "No LSP diagnostics reported."
-  end
-  local lines = { "--- LSP Diagnostics ---" }
-  for _, d in ipairs(diags) do
-    local sev = vim.diagnostic.severity[d.severity] or d.severity
-    lines[#lines+1] = string.format("Line %d [%s]: %s", d.lnum + 1, sev, d.message)
-  end
-  return table.concat(lines, "\n")
-end
-
-function M.lsp_check_file_content(path, new_content, timeout_ms)
-  local filetype = guess_filetype(path) or "plaintext"
-
-  local bufnr = create_scratch_buffer(path, new_content)
-  if not bufnr then
-    return "(LSP) Could not create scratch buffer."
-  end
-
-  local client_id, err = attach_existing_lsp_client(bufnr, filetype)
-  if not client_id then
-    api.nvim_buf_delete(bufnr, { force = true })
-    return "(LSP) " .. (err or "No suitable LSP client.")
-  end
-
-  local err2 = send_did_open(bufnr, client_id, path, filetype)
-  if err2 then
-    api.nvim_buf_delete(bufnr, { force = true })
-    return "(LSP) " .. err2
-  end
-
-  -- Optionally do a didChange
-  send_did_change(bufnr, client_id)
-
-  local diags = wait_for_diagnostics(bufnr, timeout_ms or 2000)
-  local diag_str = diagnostics_to_string(diags)
-
-  api.nvim_buf_delete(bufnr, { force = true })
-  return diag_str
-end
-
-return M
diff --git a/lua/chatgpt_nvim/tools/manager.lua b/lua/chatgpt_nvim/tools/manager.lua
deleted file mode 100644
index 50d4f62..0000000
--- a/lua/chatgpt_nvim/tools/manager.lua
+++ /dev/null
@@ -1,79 +0,0 @@
-local tools_module = require("chatgpt_nvim.tools")
-
-local M = {}
-
-local function is_destructive_command(cmd)
-  if not cmd then return false end
-  local destructive_list = { "rm", "sudo", "mv", "cp" }
-  for _, keyword in ipairs(destructive_list) do
-    if cmd:match("(^" .. keyword .. "[%s$])") or cmd:match("[%s]" .. keyword .. "[%s$]") then
-      return true
-    end
-  end
-  return false
-end
-
-local function prompt_user_tool_accept(tool_call, conf)
-  local auto_accept = conf.tool_auto_accept[tool_call.tool]
-
-  -- If this is an executeCommand and we see it's destructive, force a user prompt
-  if tool_call.tool == "executeCommand" and auto_accept then
-    if is_destructive_command(tool_call.command) then
-      auto_accept = false
-    end
-  end
-
-  if auto_accept then
-    -- If auto-accepted and not destructive, no prompt needed
-    return true
-  else
-    -- Build some context about the tool request
-    local msg = ("Tool request: %s\n"):format(tool_call.tool or "unknown")
-    if tool_call.path then
-      msg = msg .. ("Path: %s\n"):format(tool_call.path)
-    end
-    if tool_call.command then
-      msg = msg .. ("Command: %s\n"):format(tool_call.command)
-    end
-    if tool_call.replacements then
-      msg = msg .. ("Replacements: %s\n"):format(vim.inspect(tool_call.replacements))
-    end
-
-    msg = msg .. "Accept this tool request? [y/N]: "
-
-    -- Force a screen redraw so the user sees the prompt properly
-    vim.cmd("redraw")
-
-    local ans = vim.fn.input(msg)
-    return ans:lower() == "y"
-  end
-end
-
-local function handle_tool_calls(tools, conf, is_subpath_fn, read_file_fn)
-  local messages = {}
-
-  for _, call in ipairs(tools) do
-    local accepted = prompt_user_tool_accept(call, conf)
-    if not accepted then
-      table.insert(messages, ("Tool [%s] was rejected by user."):format(call.tool or "nil"))
-    else
-      local tool_impl = tools_module.tools_by_name[call.tool]
-      if tool_impl then
-        local msg = tool_impl.run(call, conf, prompt_user_tool_accept, is_subpath_fn, read_file_fn)
-        table.insert(messages, msg)
-      else
-        table.insert(messages, ("Unknown tool type: '%s'"):format(call.tool or "nil"))
-      end
-    end
-  end
-
-  local combined = table.concat(messages, "\n\n")
-  local limit = conf.prompt_char_limit or 8000
-  if #combined > limit then
-    return ("The combined tool output is too large (%d chars). Please break down the operations into smaller steps."):format(#combined)
-  end
-  return combined
-end
-
-M.handle_tool_calls = handle_tool_calls
-return M
diff --git a/lua/chatgpt_nvim/tools/read_file.lua b/lua/chatgpt_nvim/tools/read_file.lua
deleted file mode 100644
index 5519b20..0000000
--- a/lua/chatgpt_nvim/tools/read_file.lua
+++ /dev/null
@@ -1,17 +0,0 @@
-local uv = vim.loop
-local M = {}
-
-M.run = function(tool_call, conf, prompt_user_tool_accept, is_subpath, read_file)
-  local path = tool_call.path
-  if not path then
-    return "[read_file] Missing 'path'."
-  end
-  local file_data = read_file(path)
-  if file_data then
-    return string.format("Tool [read_file for '%s'] Result:\n\n%s", path, file_data)
-  else
-    return string.format("Tool [read_file for '%s'] FAILED. File not found or not readable.", path)
-  end
-end
-
-return M
diff --git a/lua/chatgpt_nvim/tools/replace_in_file.lua b/lua/chatgpt_nvim/tools/replace_in_file.lua
deleted file mode 100644
index 976f360..0000000
--- a/lua/chatgpt_nvim/tools/replace_in_file.lua
+++ /dev/null
@@ -1,51 +0,0 @@
-local handler = require("chatgpt_nvim.handler")
-local robust_lsp = require("chatgpt_nvim.tools.lsp_robust_diagnostics")
-
-local M = {}
-
-local function search_and_replace(original, replacements)
-  local updated = original
-  for _, r in ipairs(replacements) do
-    local search_str = r.search or ""
-    local replace_str = r.replace or ""
-    updated = updated:gsub(search_str, replace_str)
-  end
-  return updated
-end
-
-M.run = function(tool_call, conf, prompt_user_tool_accept, is_subpath, read_file)
-  local path = tool_call.path
-  local replacements = tool_call.replacements or {}
-
-  if not path or #replacements == 0 then
-    return "[replace_in_file] Missing 'path' or 'replacements'."
-  end
-  local root = vim.fn.getcwd()
-
-  if not is_subpath(root, path) then
-    return string.format("Tool [replace_in_file for '%s'] REJECTED. Path outside project root.", path)
-  end
-
-  local orig_data = read_file(path)
-  if not orig_data then
-    return string.format("[replace_in_file for '%s'] FAILED. Could not read file.", path)
-  end
-
-  local updated_data = search_and_replace(orig_data, replacements)
-  handler.write_file(path, updated_data, conf)
-
-  local msg = {}
-  msg[#msg+1] = string.format("[replace_in_file for '%s'] Result:\nThe content was successfully saved to %s.", path, path)
-  msg[#msg+1] = "\nHere is the full, updated content of the file that was saved:\n"
-  msg[#msg+1] = string.format("<final_file_content path=\"%s\">\n%s\n</final_file_content>", path, updated_data)
-  msg[#msg+1] = "\nIMPORTANT: For any future changes to this file, use the final_file_content shown above as your reference.\n"
-
-  if conf.auto_lint then
-    local diag_str = robust_lsp.lsp_check_file_content(path, updated_data, 3000)
-    msg[#msg+1] = "\n" .. diag_str
-  end
-
-  return table.concat(msg, "")
-end
-
-return M