refactor: Complete modular migration from kickstart.nvim

Major architectural overhaul to transform the flat kickstart.nvim structure
  into a maintainable, modular configuration while preserving upstream sync capability.

  ## Structure Changes
  - Migrated from flat `lua/custom/` to organized `lua/core/` and `lua/plugins/`
  - Separated plugin specs from configs: `lua/plugins/spec/` and `lua/plugins/config/`
  - Complex configs (LSP, Debug) now use directory structure with sub-modules:
    - `lsp/init.lua`, `lsp/servers.lua`, `lsp/keymaps.lua`
    - `debug/init.lua`, `debug/adapters.lua`, `debug/keymaps.lua`

  ## Core Improvements
  - Created dedicated core modules: options, keymaps, autocmds, bootstrap, health
  - Added comprehensive health check (`lua/core/health.lua`) for diagnostics
  - Simplified init.lua to just orchestrate module loading
  - Better separation of concerns throughout

  ## Plugin Updates
  - Fixed Blink.cmp configuration (removed invalid fuzzy options)
  - Integrated Copilot with Blink.cmp for unified completion experience
  - Added autopairs and indent-line from kickstart examples
  - Optimized for Nix development environments (removed venv assumptions)

  ## Documentation
  - Updated README with modular structure and kickstart sync instructions
  - Created comprehensive KEYBIND_ANALYSIS.md with all mappings
  - Added modular.txt help documentation
  - Created TODO_TEST.md checklist for testing

  ## Benefits
  - Easier to maintain and extend
  - Clean separation allows upstream kickstart merges without conflicts
  - Scalable architecture for adding new languages/tools
  - Better code organization and discoverability

  All kickstart functionality preserved while gaining modularity and maintainability.

lua/plugins/spec/autopairs.lua

@@ -0,0 +1,24 @@
+-- Auto-pairs - Automatically close brackets, quotes, etc.
+return {
+  'windwp/nvim-autopairs',
+  event = 'InsertEnter',
+  opts = {
+    check_ts = true,
+    ts_config = {
+      lua = { 'string', 'source' },
+      javascript = { 'string', 'template_string' },
+    },
+    disable_filetype = { 'TelescopePrompt', 'spectre_panel' },
+    fast_wrap = {
+      map = '<M-e>',
+      chars = { '{', '[', '(', '"', "'" },
+      pattern = string.gsub([[ [%'%"%)%>%]%)%}%,] ]], '%s+', ''),
+      offset = 0,
+      end_key = '$',
+      keys = 'qwertyuiopzxcvbnmasdfghjkl',
+      check_comma = true,
+      highlight = 'PmenuSel',
+      highlight_grey = 'LineNr',
+    },
+  },
+}

lua/plugins/spec/blink.lua

@@ -0,0 +1,12 @@
+-- Blink.cmp - Modern completion plugin
+return {
+  'saghen/blink.cmp',
+  lazy = false, -- Lazy loading handled internally
+  dependencies = {
+    'giuxtaposition/blink-cmp-copilot',
+  },
+  version = 'v0.*', -- Use stable releases
+  config = function()
+    require('plugins.config.blink').setup()
+  end,
+}

lua/plugins/spec/copilot.lua

@@ -0,0 +1,21 @@
+-- GitHub Copilot integration
+return {
+  'zbirenbaum/copilot.lua',
+  cmd = 'Copilot',
+  event = 'InsertEnter',
+  opts = {
+    suggestion = { enabled = false }, -- Disable inline ghost text (handled by blink.cmp)
+    panel = { enabled = false },      -- Disable panel view
+    filetypes = {
+      yaml = false,
+      markdown = false,
+      help = false,
+      gitcommit = false,
+      gitrebase = false,
+      hgcommit = false,
+      svn = false,
+      cvs = false,
+      ['.'] = false,
+    },
+  },
+}

lua/plugins/spec/debug.lua

@@ -0,0 +1,20 @@
+-- Debug Adapter Protocol (DAP) support
+return {
+  'mfussenegger/nvim-dap',
+  dependencies = {
+    -- DAP UI
+    {
+      'rcarriga/nvim-dap-ui',
+      dependencies = { 'nvim-neotest/nvim-nio' },
+    },
+    
+    -- Virtual text for debugging
+    {
+      'theHamsta/nvim-dap-virtual-text',
+      opts = {},
+    },
+  },
+  config = function()
+    require('plugins.config.debug').setup()
+  end,
+}

lua/plugins/spec/editor.lua

@@ -0,0 +1,36 @@
+-- Editor enhancement plugins
+return {
+  -- Collection of various small independent plugins/modules
+  {
+    'echasnovski/mini.nvim',
+    config = function()
+      require('plugins.config.editor').setup_mini()
+    end,
+  },
+
+  -- Highlight, edit, and navigate code
+  {
+    'nvim-treesitter/nvim-treesitter-textobjects',
+    event = 'VeryLazy',
+    dependencies = { 'nvim-treesitter/nvim-treesitter' },
+  },
+
+  -- Detect tabstop and shiftwidth automatically
+  { 'tpope/vim-sleuth' },
+
+  -- Comment plugin
+  {
+    'numToStr/Comment.nvim',
+    event = 'VeryLazy',
+    opts = {},
+  },
+
+  -- Highlight word under cursor
+  {
+    'RRethy/vim-illuminate',
+    event = { 'BufReadPost', 'BufNewFile' },
+    config = function()
+      require('plugins.config.editor').setup_illuminate()
+    end,
+  },
+}

lua/plugins/spec/formatting.lua

@@ -0,0 +1,40 @@
+-- Formatter configuration
+
+return {
+    -- ========================================
+    -- Formatter Configuration (conform.nvim)
+    -- ========================================
+    {
+        'stevearc/conform.nvim',
+        event = 'BufWritePre', -- Format on save
+        -- cmd = { 'ConformInfo' }, -- Optional: If you want the command available
+        -- keys = { ... } -- Optional: Define keys if needed
+        opts = {
+            formatters_by_ft = {
+                lua = { 'stylua' },
+                c = { 'clang_format' },
+                cpp = { 'clang_format' },
+                -- Use ruff for Python formatting (includes isort and is faster than black
+                -- Ensure 'ruff' is installed via Home Manager (pkgs.ruff)
+                python = { 'ruff_format', 'ruff_fix' },
+                -- python = { 'isort', 'black' },
+                nix = { 'alejandra' }, -- Add nix formatter
+                -- Add other filetypes and formatters, e.g.:
+                -- javascript = { "prettier" },
+                -- typescript = { "prettier" },
+                -- css = { "prettier" },
+                -- html = { "prettier" },
+                -- json = { "prettier" },
+                -- yaml = { "prettier" },
+                -- markdown = { "prettier" },
+                -- bash = { "shfmt" },
+            },
+            -- Configure format_on_save behavior
+            format_on_save = {
+                -- I recommend these options, but adjust to your liking
+                timeout_ms = 500,    -- Stop formatting if it takes too long
+                lsp_fallback = true, -- Fallback to LSP formatting if conform fails
+            },
+        },
+    },
+}

lua/plugins/spec/git.lua

@@ -0,0 +1,26 @@
+-- Git integration plugins
+return {
+  -- Fugitive - Git integration
+  {
+    'tpope/vim-fugitive',
+    cmd = { 'Git', 'G', 'Gdiff', 'Gread', 'Gwrite', 'Ggrep', 'GMove', 'GDelete', 'GBrowse', 'GRemove' },
+    keys = {
+      { '<leader>gs', '<cmd>Git<cr>', desc = 'Git status' },
+      { '<leader>gd', '<cmd>Gdiff<cr>', desc = 'Git diff' },
+      { '<leader>gc', '<cmd>Git commit<cr>', desc = 'Git commit' },
+      { '<leader>gb', '<cmd>Git blame<cr>', desc = 'Git blame' },
+      { '<leader>gl', '<cmd>Git log<cr>', desc = 'Git log' },
+      { '<leader>gp', '<cmd>Git push<cr>', desc = 'Git push' },
+      { '<leader>gf', '<cmd>Git fetch<cr>', desc = 'Git fetch' },
+    },
+  },
+  
+  -- Gitsigns - Git gutter and hunk operations
+  {
+    'lewis6991/gitsigns.nvim',
+    event = 'VeryLazy',
+    config = function()
+      require('plugins.config.git').setup_gitsigns()
+    end,
+  },
+}

lua/plugins/spec/indent-line.lua

@@ -0,0 +1,33 @@
+-- Indent guides - Show vertical lines at indentation levels
+return {
+  'lukas-reineke/indent-blankline.nvim',
+  event = { 'BufReadPost', 'BufNewFile' },
+  main = 'ibl',
+  opts = {
+    indent = {
+      char = '│',
+      tab_char = '│',
+    },
+    scope = {
+      enabled = true,
+      show_start = true,
+      show_end = false,
+      injected_languages = false,
+      highlight = { 'Function', 'Label' },
+    },
+    exclude = {
+      filetypes = {
+        'help',
+        'alpha',
+        'dashboard',
+        'neo-tree',
+        'Trouble',
+        'lazy',
+        'mason',
+        'notify',
+        'toggleterm',
+        'lazyterm',
+      },
+    },
+  },
+}

lua/plugins/spec/init.lua

@@ -0,0 +1,25 @@
+-- Main plugin loader - imports all plugin specifications
+return {
+  -- UI and Theme
+  { import = 'plugins.spec.ui' },
+  { import = 'plugins.spec.editor' },
+  { import = 'plugins.spec.autopairs' },
+  { import = 'plugins.spec.indent-line' },
+  
+  -- Core functionality
+  { import = 'plugins.spec.lsp' },
+  { import = 'plugins.spec.treesitter' },
+  { import = 'plugins.spec.telescope' },
+  { import = 'plugins.spec.blink' },
+  
+  -- Git integration
+  { import = 'plugins.spec.git' },
+  
+  -- Development tools
+  { import = 'plugins.spec.copilot' },
+  { import = 'plugins.spec.debug' },
+  { import = 'plugins.spec.formatting' },
+  
+  -- Navigation
+  { import = 'plugins.spec.nvim-tmux-navigator' },
+}

lua/plugins/spec/lsp.lua

@@ -0,0 +1,26 @@
+-- LSP Plugin Specification
+return {
+  {
+    'neovim/nvim-lspconfig',
+    event = { 'BufReadPost', 'BufNewFile' },
+    dependencies = {
+      { 'j-hui/fidget.nvim', opts = {} },
+      'folke/lazydev.nvim',
+    },
+    config = function()
+      require('plugins.config.lsp').setup()
+    end,
+  },
+
+  -- LazyDev for better Neovim Lua development
+  {
+    'folke/lazydev.nvim',
+    ft = 'lua',
+    opts = {
+      library = {
+        { path = 'luvit-meta/library', words = { 'vim%.uv' } },
+      },
+    },
+  },
+}
+

lua/plugins/spec/nvim-tmux-navigator.lua

@@ -0,0 +1,11 @@
+-- Tmux navigation integration
+return {
+  'christoomey/vim-tmux-navigator',
+  keys = {
+    { '<C-h>', ':TmuxNavigateLeft<CR>', desc = 'Navigate to left tmux pane' },
+    { '<C-j>', ':TmuxNavigateDown<CR>', desc = 'Navigate to down tmux pane' },
+    { '<C-k>', ':TmuxNavigateUp<CR>', desc = 'Navigate to up tmux pane' },
+    { '<C-l>', ':TmuxNavigateRight<CR>', desc = 'Navigate to right tmux pane' },
+    { '<C-\\>', ':TmuxNavigatePrevious<CR>', desc = 'Navigate to previous tmux pane' },
+  },
+}

lua/plugins/spec/telescope.lua

@@ -0,0 +1,21 @@
+-- Telescope - Fuzzy finder
+return {
+  'nvim-telescope/telescope.nvim',
+  event = 'VimEnter',
+  branch = '0.1.x',
+  dependencies = {
+    'nvim-lua/plenary.nvim',
+    {
+      'nvim-telescope/telescope-fzf-native.nvim',
+      build = 'make',
+      cond = function()
+        return vim.fn.executable 'make' == 1
+      end,
+    },
+    { 'nvim-telescope/telescope-ui-select.nvim' },
+    { 'nvim-tree/nvim-web-devicons', enabled = vim.g.have_nerd_font },
+  },
+  config = function()
+    require('plugins.config.telescope').setup()
+  end,
+}

lua/plugins/spec/treesitter.lua

@@ -0,0 +1,45 @@
+-- Treesitter - Syntax highlighting and text objects
+return {
+  'nvim-treesitter/nvim-treesitter',
+  event = { 'BufReadPost', 'BufNewFile' },
+  build = ':TSUpdate',
+  main = 'nvim-treesitter.configs',
+  opts = {
+    ensure_installed = {
+      'bash',
+      'c',
+      'cmake',
+      'cpp',
+      'diff',
+      'html',
+      'lua',
+      'luadoc',
+      'make',
+      'markdown',
+      'markdown_inline',
+      'nix',
+      'python',
+      'query',
+      'vim',
+      'vimdoc',
+      'yaml',
+    },
+    auto_install = true,
+    highlight = {
+      enable = true,
+      additional_vim_regex_highlighting = false,
+    },
+    indent = {
+      enable = true,
+    },
+    incremental_selection = {
+      enable = true,
+      keymaps = {
+        init_selection = '<c-space>',
+        node_incremental = '<c-space>',
+        scope_incremental = false,
+        node_decremental = '<bs>',
+      },
+    },
+  },
+}

lua/plugins/spec/ui.lua

@@ -0,0 +1,29 @@
+-- UI and Theme plugins
+return {
+  -- Color scheme
+  {
+    'folke/tokyonight.nvim',
+    priority = 1000,
+    init = function()
+      vim.cmd.colorscheme 'tokyonight-night'
+      vim.cmd.hi 'Comment gui=none'
+    end,
+  },
+
+  -- Which-key for keybind hints
+  {
+    'folke/which-key.nvim',
+    event = 'VimEnter',
+    config = function()
+      require('plugins.config.ui').setup_which_key()
+    end,
+  },
+
+  -- Todo comments highlighting
+  {
+    'folke/todo-comments.nvim',
+    event = 'VimEnter',
+    dependencies = { 'nvim-lua/plenary.nvim' },
+    opts = { signs = false }
+  },
+}