refactor(config/nvim): move pack.add declarations into individual plugin files

The monolithic vim.pack.add() table in init.lua was removed and each
plugin/*.lua file now declares its own dependencies via vim.pack.add()
at the top. tools.lua was decomposed into per-plugin files (cmake.lua,
jupynvim.lua, just.lua, kulala.lua, mise.lua, neogit.lua, sshfs.lua,
trouble.lua, undotree.lua, zoxide.lua) each with their own config and
keymaps. This makes plugin files self-contained and easier to maintain.

config/nvim/init.lua

@@ -114,96 +114,14 @@ vim.filetype.add({
 })
 
 vim.pack.add({
-    { src = 'https://github.com/3rd/image.nvim' },
-	{ src = "https://github.com/folke/snacks.nvim" },
-    { src = "https://github.com/folke/trouble.nvim" },
-    { src = "https://github.com/olimorris/codecompanion.nvim" },
-    { src = 'https://github.com/Civitasv/cmake-tools.nvim' },
-    { src = 'https://github.com/Davidyz/VectorCode' },
-    { src = 'https://github.com/Glhou/jjsigns.nvim', version = 'fix/skip-extra-lines' },
-    { src = 'https://github.com/HakonHarnes/img-clip.nvim' },
-    { src = 'https://github.com/JoosepAlviste/nvim-ts-context-commentstring' },
-    { src = 'https://github.com/L3MON4D3/LuaSnip' },
-    { src = 'https://github.com/MeanderingProgrammer/render-markdown.nvim' },
-    { src = 'https://github.com/MeanderingProgrammer/render-markdown.nvim' },
     { src = 'https://github.com/MunifTanjim/nui.nvim' },
-    { src = 'https://github.com/NeogitOrg/neogit' },
-    { src = 'https://github.com/PhantomYdn/fabric-ai.nvim' },
-    { src = 'https://github.com/Saecki/crates.nvim' },
-    { src = 'https://github.com/Saghen/blink.cmp', version = vim.version.range('1.*') },
-    { src = 'https://github.com/SjB/orgmode', version = 'sjb-wip' }, 
     { src = 'https://github.com/SmiteshP/nvim-navic' },
-    { src = 'https://github.com/WhoIsSethDaniel/mason-tool-installer.nvim' },
-    { src = 'https://github.com/akinsho/org-bullets.nvim' },
-    { src = 'https://github.com/akinsho/toggleterm.nvim' },
-    { src = 'https://github.com/SjB/codecompanion-agentskills.nvim', version = 'support_disable_model_invocation_flag' },
-    { src = 'https://github.com/carlos-algms/agentic.nvim' },
-    { src = 'https://github.com/chipsenkbeil/org-roam.nvim' },
-    { src = 'https://github.com/christoomey/vim-tmux-navigator' },
---    { src = 'https://github.com/copilotlsp-nvim/copilot-lsp' },
     { src = 'https://github.com/esmuellert/codediff.nvim' },
-    { src = 'https://github.com/fang2hou/blink-copilot' },
-    { src = 'https://github.com/folke/flash.nvim' },
-    { src = 'https://github.com/folke/persistence.nvim' },
     { src = 'https://github.com/folke/todo-comments.nvim' },
-    { src = 'https://github.com/folke/which-key.nvim' },
-    { src = 'https://github.com/franco-ruggeri/codecompanion-spinner.nvim' },
-    { src = 'https://github.com/hat0uma/csvview.nvim' },
-    { src = 'https://github.com/hedyhli/outline.nvim' },
-    { src = 'https://github.com/iamcco/markdown-preview.nvim' },
     { src = 'https://github.com/j-hui/fidget.nvim' },
-    { src = 'https://github.com/jay-babu/mason-nvim-dap.nvim' },
-    { src = 'https://github.com/julienvincent/hunk.nvim' },
-    { src = 'https://github.com/lervag/vimtex' },
-    { src = 'https://github.com/lewis6991/gitsigns.nvim' },
-    { src = 'https://github.com/mbbill/undotree' },
-    { src = 'https://github.com/SjB/meow.review.nvim', version = 'fix-invalid-buffer-id' },
-    { src = 'https://github.com/mfussenegger/nvim-ansible' },
-    { src = 'https://github.com/mfussenegger/nvim-dap' },
-    { src = 'https://github.com/mistweaverco/kulala.nvim' },
-    { src = 'https://github.com/moyiz/blink-emoji.nvim' },
-    { src = 'https://github.com/neovim/nvim-lspconfig' },
     { src = 'https://github.com/norcalli/nvim-colorizer.lua' },
     { src = 'https://github.com/nvim-lua/plenary.nvim' }, 
-    { src = 'https://github.com/nvim-lualine/lualine.nvim' },
-    { src = 'https://github.com/nvim-mini/mini.ai' },
-    { src = 'https://github.com/nvim-mini/mini.align' },
-    { src = 'https://github.com/nvim-mini/mini.bracketed' },
-    { src = 'https://github.com/nvim-mini/mini.extra' },
-    { src = 'https://github.com/nvim-mini/mini.files' },
-    { src = 'https://github.com/nvim-mini/mini.hipatterns' },
-    { src = 'https://github.com/nvim-mini/mini.move' },
-    { src = 'https://github.com/nvim-mini/mini.operators' },
-    { src = 'https://github.com/nvim-mini/mini.sessions' },
-    { src = 'https://github.com/nvim-mini/mini.splitjoin' },
-    { src = 'https://github.com/nvim-mini/mini.surround' },
     { src = 'https://github.com/nvim-neotest/nvim-nio' },
-    { src = 'https://github.com/nvim-pack/nvim-spectre' },
     { src = 'https://github.com/nvim-tree/nvim-web-devicons' },
-    { src = 'https://github.com/nvim-treesitter/nvim-treesitter', version = 'main' },
-    { src = 'https://github.com/nvim-treesitter/nvim-treesitter-context' },
-    { src = 'https://github.com/nvim-treesitter/nvim-treesitter-context' },
-    { src = 'https://github.com/nvim-treesitter/nvim-treesitter-textobjects', version = 'main' },
-    { src = 'https://github.com/romus204/tree-sitter-manager.nvim' },
-    { src = 'https://github.com/otavioschwanck/arrow.nvim' },
-    { src = 'https://github.com/rafamadriz/friendly-snippets' },
-    { src = 'https://github.com/rafikdraoui/jj-diffconflicts' },
-    { src = 'https://github.com/ravitemer/codecompanion-history.nvim' },
-    { src = 'https://github.com/ravitemer/codecompanion-history.nvim' },
-    { src = 'https://github.com/rcarriga/nvim-dap-ui' },
-    { src = 'https://github.com/salkin-mada/openscad.nvim' },
-    { src = 'https://github.com/sheng-tse/jupynvim' },
-    { src = 'https://github.com/sindrets/diffview.nvim' },
-    { src = 'https://github.com/stevearc/conform.nvim' },
-    { src = 'https://github.com/stevearc/overseer.nvim' },
-    { src = 'https://github.com/stevearc/quicker.nvim' },
-    { src = 'https://github.com/ten3roberts/window-picker.nvim' },
-    { src = 'https://github.com/thunder-coding/zincoxide' },
-    { src = 'https://github.com/ttgrules/cc-adapter-copilot-cli-acp' },
-    { src = 'https://github.com/uhs-robert/sshfs.nvim' },
-    { src = 'https://github.com/utilyre/barbecue.nvim' },
-    { src = 'https://github.com/williamboman/mason-lspconfig.nvim' },
-    { src = 'https://github.com/williamboman/mason.nvim' },
-    { src = 'https://github.com/zbirenbaum/copilot.lua' },
-    { src = 'https://plugins.ejri.dev/mise.nvim' },
 })
+

config/nvim/plugin/agentic.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/carlos-algms/agentic.nvim' },
+})
+
 require('agentic').setup({
     -- Available by default: "claude-agent-acp" | "gemini-acp" | "codex-acp" | "opencode-acp" | "cursor-acp" | "auggie-acp" | "mistral-vibe-acp"
     provider = "opencode-acp", -- setting the name here is all you need to get started

config/nvim/plugin/arrow.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/otavioschwanck/arrow.nvim' },
+})
+
 require('arrow').setup({
     show_icons = true,
     leader_key = ';', -- Recommended to be a single key

config/nvim/plugin/barbecue.lua

@@ -1 +1,4 @@
+vim.pack.add({
+    { src = 'https://github.com/utilyre/barbecue.nvim' },
+})
 require('barbecue').setup()

config/nvim/plugin/blink.lua

@@ -1,3 +1,9 @@
+vim.pack.add({
+    { src = 'https://github.com/Saghen/blink.cmp', version = vim.version.range('1.*') },
+    { src = 'https://github.com/fang2hou/blink-copilot' },
+    { src = 'https://github.com/moyiz/blink-emoji.nvim' },
+})
+
 require('blink.cmp').setup({
     enabled = function()
         local filetype = vim.bo[0].filetype

config/nvim/plugin/cmake.lua

@@ -0,0 +1,183 @@
+vim.pack.add({
+    { src = 'https://github.com/Civitasv/cmake-tools.nvim' },
+    { src = 'https://github.com/stevearc/overseer.nvim' },
+})
+
+require("overseer").setup({
+    templates = { "builtin", "user" },
+    component_aliases = {
+        default = {
+            { 'display_duration', detail_level = 2 },
+            'on_output_summarize',
+            'on_exit_set_status',
+            'on_complete_notify',
+            'on_result_diagnostics',
+            {'on_result_diagnostics_quickfix', open = true, close = true},
+        },
+        default_vscode = {
+            'default',
+            'on_result_diagnostics',
+            {'on_result_diagnostics_quickfix', open = true, close = true},
+            'on_complete_notify',
+        },
+    }
+})
+
+-- local pm = require("overseer.template.vscode.problem_matcher")
+-- pm.register_problem_matcher("$rustc", {
+    --      fileLocation = { "autoDetect", "${cwd}" },
+    --      pattern = {
+        --          --regexp = "^(.*?)-->\\s+(.*?):(\\d+):(\\d+)$",
+        --          -- vim_regexp = "\\v^(.*?)-->\\s+(.*?):(\\d+):(\\d+)$",
+        --          regexp = "^\\s+-->\\s*([^:]*):(\\d+):(\\d+)$",
+        --          vim_regexp = "\\v^\\s+-->\\s*([^:]*):(\\d+):(\\d+)$",
+        --          file = 1,
+        --          line = 2,
+        --          column = 3,
+        --      }
+        -- })
+
+local osys = require("cmake-tools.osys")
+require("cmake-tools").setup {
+    cmake_command = "cmake", -- this is used to specify cmake command path
+    ctest_command = "ctest", -- this is used to specify ctest command path
+    cmake_use_preset = true,
+    cmake_regenerate_on_save = true, -- auto generate when save CMakeLists.txt
+    cmake_generate_options = { "-DCMAKE_EXPORT_COMPILE_COMMANDS=1" }, -- this will be passed when invoke `CMakeGenerate`
+    cmake_build_options = {}, -- this will be passed when invoke `CMakeBuild`
+    -- support macro expansion:
+    --       ${kit}
+    --       ${kitGenerator}
+    --       ${variant:xx}
+    cmake_build_directory = function()
+        if osys.iswin32 then
+            return "out\\${variant:buildType}"
+        end
+        return "out/${variant:buildType}"
+    end, -- this is used to specify generate directory for cmake, allows macro expansion, can be a string or a function returning the string, relative to cwd.
+    cmake_soft_link_compile_commands = true, -- this will automatically make a soft link from compile commands file to project root dir
+    cmake_compile_commands_from_lsp = false, -- this will automatically set compile commands file location using lsp, to use it, please set `cmake_soft_link_compile_commands` to false
+    cmake_kits_path = nil, -- this is used to specify global cmake kits path, see CMakeKits for detailed usage
+    cmake_variants_message = {
+        short = { show = true }, -- whether to show short message
+        long = { show = true, max_length = 40 }, -- whether to show long message
+    },
+    cmake_dap_configuration = { -- debug settings for cmake
+        name = "cpp",
+        type = "codelldb",
+        request = "launch",
+        stopOnEntry = false,
+        runInTerminal = true,
+        console = "integratedTerminal",
+    },
+    cmake_executor = { -- executor to use
+        name = "quickfix", -- name of the executor
+        opts = {}, -- the options the executor will get, possible values depend on the executor type. See `default_opts` for possible values.
+        default_opts = { -- a list of default and possible values for executors
+            quickfix = {
+                show = "always", -- "always", "only_on_error"
+                position = "belowright", -- "vertical", "horizontal", "leftabove", "aboveleft", "rightbelow", "belowright", "topleft", "botright", use `:h vertical` for example to see help on them
+                size = 10,
+                encoding = "utf-8", -- if encoding is not "utf-8", it will be converted to "utf-8" using `vim.fn.iconv`
+                auto_close_when_success = true, -- typically, you can use it with the "always" option; it will auto-close the quickfix buffer if the execution is successful.
+            },
+            toggleterm = {
+                direction = "float", -- 'vertical' | 'horizontal' | 'tab' | 'float'
+                close_on_exit = false, -- whether close the terminal when exit
+                auto_scroll = true, -- whether auto scroll to the bottom
+                singleton = true, -- single instance, autocloses the opened one, if present
+            },
+            overseer = {
+                new_task_opts = {
+                    strategy = {
+                        "toggleterm",
+                        direction = "horizontal",
+                        autos_croll = true,
+                        quit_on_exit = "success"
+                    }
+                }, -- options to pass into the `overseer.new_task` command
+                on_new_task = function(task)
+                    require("overseer").open(
+                        { enter = false, direction = "right" }
+                    )
+                end,   -- a function that gets overseer.Task when it is created, before calling `task:start`
+            },
+            terminal = {
+                name = "Main Terminal",
+                prefix_name = "[CMakeTools]: ", -- This must be included and must be unique, otherwise the terminals will not work. Do not use a simple spacebar " ", or any generic name
+                split_direction = "horizontal", -- "horizontal", "vertical"
+                split_size = 11,
+
+                -- Window handling
+                single_terminal_per_instance = true, -- Single viewport, multiple windows
+                single_terminal_per_tab = true, -- Single viewport per tab
+                keep_terminal_static_location = true, -- Static location of the viewport if avialable
+                auto_resize = true, -- Resize the terminal if it already exists
+
+                -- Running Tasks
+                start_insert = false, -- If you want to enter terminal with :startinsert upon using :CMakeRun
+                focus = false, -- Focus on terminal when cmake task is launched.
+                do_not_add_newline = false, -- Do not hit enter on the command inserted when using :CMakeRun, allowing a chance to review or modify the command before hitting enter.
+            }, -- terminal executor uses the values in cmake_terminal
+        },
+    },
+    cmake_runner = { -- runner to use
+        name = "terminal", -- name of the runner
+        opts = {}, -- the options the runner will get, possible values depend on the runner type. See `default_opts` for possible values.
+        default_opts = { -- a list of default and possible values for runners
+            quickfix = {
+                show = "always", -- "always", "only_on_error"
+                position = "belowright", -- "bottom", "top"
+                size = 10,
+                encoding = "utf-8",
+                auto_close_when_success = true, -- typically, you can use it with the "always" option; it will auto-close the quickfix buffer if the execution is successful.
+            },
+            toggleterm = {
+                direction = "float", -- 'vertical' | 'horizontal' | 'tab' | 'float'
+                close_on_exit = false, -- whether close the terminal when exit
+                auto_scroll = true, -- whether auto scroll to the bottom
+                singleton = true, -- single instance, autocloses the opened one, if present
+            },
+            overseer = {
+                new_task_opts = {
+                    strategy = {
+                        "toggleterm",
+                        direction = "horizontal",
+                        autos_croll = true,
+                        quit_on_exit = "success"
+                    }
+                }, -- options to pass into the `overseer.new_task` command
+                on_new_task = function(task)
+                end,   -- a function that gets overseer.Task when it is created, before calling `task:start`
+            },
+            terminal = {
+                name = "Main Terminal",
+                prefix_name = "[CMakeTools]: ", -- This must be included and must be unique, otherwise the terminals will not work. Do not use a simple spacebar " ", or any generic name
+                split_direction = "horizontal", -- "horizontal", "vertical"
+                split_size = 11,
+
+                -- Window handling
+                single_terminal_per_instance = true, -- Single viewport, multiple windows
+                single_terminal_per_tab = true, -- Single viewport per tab
+                keep_terminal_static_location = true, -- Static location of the viewport if avialable
+                auto_resize = true, -- Resize the terminal if it already exists
+
+                -- Running Tasks
+                start_insert = false, -- If you want to enter terminal with :startinsert upon using :CMakeRun
+                focus = false, -- Focus on terminal when cmake task is launched.
+                do_not_add_newline = false, -- Do not hit enter on the command inserted when using :CMakeRun, allowing a chance to review or modify the command before hitting enter.
+            },
+        },
+    },
+    cmake_notifications = {
+        runner = { enabled = true },
+        executor = { enabled = true },
+        spinner = { "⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏" }, -- icons used for progress display
+        refresh_rate_ms = 100, -- how often to iterate icons
+    },
+    cmake_virtual_text_support = true, -- Show the target related to current file using virtual text (at right corner)
+}
+
+vim.keymap.set('n', "<leader>uo", "<cmd>OverseerToggle<CR>", { desc = "Overseer Toggle"  })
+vim.keymap.set('n', "<F5>", "<cmd>OverseerRun<CR>", { desc = "Run Overseer"  })
+vim.keymap.set('n', "<F6>", "<cmd>OverseerToggle<CR>", { desc = "Overseer Toggle"  })

config/nvim/plugin/codecompanion.lua

@@ -1,3 +1,10 @@
+vim.pack.add({
+    { src = "https://github.com/olimorris/codecompanion.nvim" },
+    { src = 'https://github.com/Davidyz/VectorCode' },
+    { src = 'https://github.com/SjB/codecompanion-agentskills.nvim', version = 'support_disable_model_invocation_flag' },
+    { src = 'https://github.com/franco-ruggeri/codecompanion-spinner.nvim' },
+    { src = 'https://github.com/ravitemer/codecompanion-history.nvim' },
+})
 
 vim.keymap.set({'n', 'v'}, '<leader>mct', '<cmd>CodeCompanionChat Toggle<cr>',  { noremap = true, silent = true, desc = "CC Toggle" })
 vim.keymap.set({'n', 'v'}, '<leader>mca', '<cmd>CodeCompanionActions<cr>',  { noremap = true, silent = true, desc = "CC Action" })

config/nvim/plugin/conform.lua

@@ -1,3 +1,6 @@
+vim.pack.add({
+    { src = 'https://github.com/stevearc/conform.nvim' },
+})
 
 local conform = require('conform')
 

config/nvim/plugin/copilot.lua

@@ -1,3 +1,8 @@
+vim.pack.add({
+    { src = 'https://github.com/ttgrules/cc-adapter-copilot-cli-acp' },
+    { src = 'https://github.com/zbirenbaum/copilot.lua' },
+--    { src = 'https://github.com/copilotlsp-nvim/copilot-lsp' },
+})
 
 vim.g.copilot_nes_debounce = 500
 

config/nvim/plugin/crates.lua

@@ -1,3 +1,6 @@
+vim.pack.add({
+    { src = 'https://github.com/Saecki/crates.nvim' },
+})  
 
 local crates = require("crates")
 local opts = { silent = true }

config/nvim/plugin/csvview.lua

@@ -1,3 +1,6 @@
+vim.pack.add({
+    { src = 'https://github.com/hat0uma/csvview.nvim' },
+})
 
 require('csvview').setup({
     parser = { comments = { "#", "//" } },

config/nvim/plugin/fabric-ai.lua

@@ -1,4 +1,8 @@
 if vim.fn.executable("fabric-ai") == 1 then
+    vim.pack.add({
+        { src = 'https://github.com/PhantomYdn/fabric-ai.nvim' },
+    })
+
     require('fabric-ai').setup({
         -- Default configuration (all optional)
         fabric_path = "fabric-ai", -- Path to Fabric CLI

config/nvim/plugin/flash.lua

@@ -1,3 +1,6 @@
+vim.pack.add({
+    { src = 'https://github.com/folke/flash.nvim' },
+})
 
 require('flash').setup({
     modes = {

config/nvim/plugin/git.lua

@@ -1,3 +1,6 @@
+vim.pack.add({
+    { src = 'https://github.com/lewis6991/gitsigns.nvim' },
+})
 
 vim.keymap.set({ 'n' }, '<leader>ug', "Gitsigns toggle_signs", { desc = 'Gitsigns toggle' })
 

config/nvim/plugin/jj.lua

@@ -1,5 +1,10 @@
 if vim.fn.executable("jj") == 1 then
-    vim.pack.add({ { src = 'https://github.com/NicolasGB/jj.nvim' } })
+    vim.pack.add({ 
+        { src = 'https://github.com/Glhou/jjsigns.nvim', version = 'fix/skip-extra-lines' },
+        { src = 'https://github.com/julienvincent/hunk.nvim' },
+        { src = 'https://github.com/NicolasGB/jj.nvim' },
+        { src = 'https://github.com/rafikdraoui/jj-diffconflicts' },
+    })
     
     local cmd = require("jj.cmd")
     local annotate = require("jj.annotate")

config/nvim/plugin/jupynvim.lua

@@ -0,0 +1,19 @@
+vim.pack.add({
+    { src = 'https://github.com/sheng-tse/jupynvim' },
+})
+
+vim.api.nvim_create_autocmd('PackChanged', { 
+    callback = function()
+        local core = vim.fn.stdpath("data") .. "/site/pack/core/opt/jupynvim/core"
+        vim.fn.system({
+            "cargo", "build", "--release",
+            "--manifest-path", core .. "/Cargo.toml",
+        })
+    end
+})
+
+require("jupynvim").setup({
+    log_level = "debug",
+    image_renderer = "placeholder",  -- "placeholder", "kitty", or "chafa"
+})
+

config/nvim/plugin/just.lua

@@ -0,0 +1,14 @@
+if vim.fn.executable("just") == 1 then
+    vim.pack.add({ { src = 'https://github.com/al1-ce/just.nvim' } })
+
+    require("just").setup({
+        fidget_message_limit = 32, -- limit for length of fidget progress message
+        open_qf_on_error = true,   -- opens quickfix when task fails
+        open_qf_on_run = true,     -- opens quickfix when running `run` task (`:JustRun`)
+        open_qf_on_any = false;    -- opens quickfix when running any task (overrides other open_qf options)
+        autoscroll_qf = true,      -- automatically scroll quickfix window on output
+        register_commands = true,  -- if set to true then commands (:Just*) will be registered
+        notify = vim.notify,       -- what to use to show messages/errors
+    })
+end
+

config/nvim/plugin/kulala.lua

@@ -0,0 +1,5 @@
+vim.pack.add({
+    { src = 'https://github.com/mistweaverco/kulala.nvim' },
+})
+
+require('kulala').setup()

config/nvim/plugin/lsp.lua

@@ -1,3 +1,13 @@
+vim.pack.add({
+    { src = 'https://github.com/williamboman/mason-lspconfig.nvim' },
+    { src = 'https://github.com/williamboman/mason.nvim' },
+    { src = 'https://github.com/neovim/nvim-lspconfig' },
+    { src = 'https://github.com/rcarriga/nvim-dap-ui' },
+    { src = 'https://github.com/mfussenegger/nvim-dap' },
+    { src = 'https://github.com/jay-babu/mason-nvim-dap.nvim' },
+    { src = 'https://github.com/WhoIsSethDaniel/mason-tool-installer.nvim' },
+})
+
 vim.keymap.set("i", "<C-.>", function()
     if not vim.lsp.inline_completion.get() then
         return "<C-.>"

config/nvim/plugin/lualine.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/nvim-lualine/lualine.nvim' },
+})
+
 local function truncate_branch_name(branch)
     if not branch or branch == "" then
         return ""

config/nvim/plugin/luasnip.lua

@@ -1,3 +1,8 @@
+vim.pack.add({
+    { src = 'https://github.com/L3MON4D3/LuaSnip' },
+    { src = 'https://github.com/rafamadriz/friendly-snippets' },
+})
+
 -- build = "make install_jsregexp",
 require('luasnip.loaders.from_vscode').lazy_load()
 require('luasnip.loaders.from_vscode').lazy_load({ paths = "./json_snippets" })

config/nvim/plugin/markdown-preview.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/iamcco/markdown-preview.nvim' },
+    { src = 'https://github.com/MeanderingProgrammer/render-markdown.nvim' },
+})
 vim.g.mkdp_filetypes = { "markdown" }
 
 vim.keymap.set("n", "<leader>xmp", "<cmd>MarkdownPreview<CR>", { desc ="Markdown Preview"  })

config/nvim/plugin/meow-review.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/SjB/meow.review.nvim', version = 'fix-invalid-buffer-id' },
+})
+
 require("meow.review").setup({
 -- Your custom configuration goes here
 })

config/nvim/plugin/mini.lua

@@ -1,3 +1,17 @@
+vim.pack.add({
+    { src = 'https://github.com/nvim-mini/mini.ai' },
+    { src = 'https://github.com/nvim-mini/mini.align' },
+    { src = 'https://github.com/nvim-mini/mini.bracketed' },
+    { src = 'https://github.com/nvim-mini/mini.extra' },
+    { src = 'https://github.com/nvim-mini/mini.files' },
+    { src = 'https://github.com/nvim-mini/mini.hipatterns' },
+    { src = 'https://github.com/nvim-mini/mini.move' },
+    { src = 'https://github.com/nvim-mini/mini.operators' },
+    { src = 'https://github.com/nvim-mini/mini.sessions' },
+    { src = 'https://github.com/nvim-mini/mini.splitjoin' },
+    { src = 'https://github.com/nvim-mini/mini.surround' },
+})
+
 local MiniExtra = require('mini.extra')
 local ai = require('mini.ai')
 local spec_treesitter = ai.gen_spec.treesitter

config/nvim/plugin/mise.lua

@@ -0,0 +1,13 @@
+if vim.fn.executable("mise") == 1 then
+    vim.pack.add({
+        { src = 'https://plugins.ejri.dev/mise.nvim' },
+    })
+
+    require('mise').setup({
+        unset_vars = true,
+        load_on_setup = true,
+        force_run = true,
+    })
+
+    vim.keymap.set({'n'}, '<leader>xM', '<cmd>Lazy reload mise.nvim<cr>', { desc = "Reload mise environment"  })
+end

config/nvim/plugin/neogit.lua

@@ -0,0 +1,25 @@
+vim.pack.add({ 
+    { src = 'https://github.com/NeogitOrg/neogit' },
+    { src = 'https://github.com/sindrets/diffview.nvim' },
+})
+
+require('neogit').setup({
+    -- disable_context_highlighting = true,
+    disable_commit_confirmation = true,
+    disable_insert_on_commit = false,
+    disable_signs = true,
+    integrations = { diffview = true, fz_lua = false },
+    auto_refresh = false,
+    console_timeout = 5000,
+    auto_show_console = false,
+    sections = {
+        stashes = {
+            folded = false,
+        },
+        recent = { folded = false },
+    },
+})
+
+vim.keymap.set({'n'}, '<leader>vn', '<cmd>Neogit kind=auto<cr>', { desc = 'Neogit' })
+vim.keymap.set({'n'}, '<leader>vN', '<cmd>Neogit kind=floating<cr>', { desc = 'Neogit' })
+

config/nvim/plugin/nvim-ansible.lua

@@ -1,2 +1,6 @@
+vim.pack.add({
+    { src = 'https://github.com/mfussenegger/nvim-ansible' },
+})
+
 vim.keymap.set('v', '<leader>xa', function() require('ansible').run() end, { buffer = true, silent = true, desc = 'execute via ansible' })
 vim.keymap.set('n', '<leader>xa', ":w<CR> :lua require('ansible').run()<CR>", { buffer = true, silent = true, desc = 'execute via ansible' })

config/nvim/plugin/openscad.lua

@@ -1,2 +1,6 @@
+vim.pack.add({
+    { src = 'https://github.com/salkin-mada/openscad.nvim' },
+})
+
 vim.g.openscad_load_snippets = true
 require("openscad").setup({})

config/nvim/plugin/orgmode.lua

@@ -1,4 +1,8 @@
-
+vim.pack.add({
+    { src = 'https://github.com/SjB/orgmode', version = 'sjb-wip' }, 
+    { src = 'https://github.com/chipsenkbeil/org-roam.nvim' },
+    { src = 'https://github.com/akinsho/org-bullets.nvim' },
+})
 require('orgmode').setup({
     ui = {
         input = {

config/nvim/plugin/outline.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/hedyhli/outline.nvim' },
+})
+
 require('outline').setup({
     symbol_folding = {
         -- Unfold entire symbol tree by default with false, otherwise enter a

config/nvim/plugin/persistence.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/folke/persistence.nvim' },
+})
+
 require("persistence").setup({
   dir = vim.fn.expand(vim.fn.stdpath("state") .. "/sessions/"), -- directory where session files are saved
   options = { "buffers", "curdir", "tabpages", "winsize" }, -- sessionoptions used when saving sessions

config/nvim/plugin/quicker.lua

@@ -1 +1,4 @@
+vim.pack.add({
+    { src = 'https://github.com/stevearc/quicker.nvim' },
+})
 require('quicker').setup()

config/nvim/plugin/snacks.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+	{ src = "https://github.com/folke/snacks.nvim" },
+})
+
 require('snacks').setup({
     animate = {
         enabled = false,

config/nvim/plugin/spectre.lua

@@ -1,3 +1,6 @@
+vim.pack.add({
+    { src = 'https://github.com/nvim-pack/nvim-spectre' },
+})
 
 vim.keymap.set({ 'n' }, "<leader>sr", function() require("spectre").open() end, { desc = "Replace in files (Spectre)" })
 

config/nvim/plugin/sshfs.lua

@@ -0,0 +1,14 @@
+
+vim.pack.add({
+    { src = 'https://github.com/uhs-robert/sshfs.nvim' },
+})
+
+require('sshfs').setup({
+    mounts = {
+        base_dir = vim.fn.expand("$HOME") .. "/Public", -- where remote mounts are created
+    },
+    lead_prefix = "<leader>t",     
+    -- Refer to the configuration section below
+    -- or leave empty for defaults
+})
+

config/nvim/plugin/toggleterm.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/akinsho/toggleterm.nvim' },
+})
+
 require("toggleterm").setup({
     -- highlights = require("rose-pine.plugins.toggleterm"),
     size = 20,

config/nvim/plugin/tools.lua

@@ -1,275 +1,12 @@
-require('kulala').setup()
+vim.pack.add({
-
+    { src = 'https://github.com/3rd/image.nvim' },
-if vim.fn.executable("just") == 1 then
+    { src = 'https://github.com/HakonHarnes/img-clip.nvim' },
-    vim.pack.add({ { src = 'https://github.com/al1-ce/just.nvim' } })
+})
-
-    require("just").setup({
-        fidget_message_limit = 32, -- limit for length of fidget progress message
-        open_qf_on_error = true,   -- opens quickfix when task fails
-        open_qf_on_run = true,     -- opens quickfix when running `run` task (`:JustRun`)
-        open_qf_on_any = false;    -- opens quickfix when running any task (overrides other open_qf options)
-        autoscroll_qf = true,      -- automatically scroll quickfix window on output
-        register_commands = true,  -- if set to true then commands (:Just*) will be registered
-        notify = vim.notify,       -- what to use to show messages/errors
-    })
-end
 
 require('img-clip').setup()
 require('image').setup({
     backend = "sixel"
 })
 
-require('sshfs').setup({
-    mounts = {
-        base_dir = vim.fn.expand("$HOME") .. "/Public", -- where remote mounts are created
-    },
-    lead_prefix = "<leader>t",     
-    -- Refer to the configuration section below
-    -- or leave empty for defaults
-})
-
-require('mise').setup({
-    unset_vars = true,
-    load_on_setup = true,
-    force_run = true,
-})
-
-require('neogit').setup({
-    -- disable_context_highlighting = true,
-    disable_commit_confirmation = true,
-    disable_insert_on_commit = false,
-    disable_signs = true,
-    integrations = { diffview = true, fz_lua = false },
-    auto_refresh = false,
-    console_timeout = 5000,
-    auto_show_console = false,
-    sections = {
-        stashes = {
-            folded = false,
-        },
-        recent = { folded = false },
-    },
-})
-
-if vim.fn.executable("zoxide") == 1 then
-    require('zincoxide').setup({
-        zincoxide_cmd = "zoxide",
-        complete = true,
-        behaviour = "tabs",
-    })
-end
-
-require('trouble').setup({
-    defaults = {
-        auto_close = true,
-        auto_open = true,
-    },
-})
-
-vim.api.nvim_create_autocmd('PackChanged', { 
-    callback = function()
-        local core = vim.fn.stdpath("data") .. "/site/pack/core/opt/jupynvim/core"
-        vim.fn.system({
-            "cargo", "build", "--release",
-            "--manifest-path", core .. "/Cargo.toml",
-        })
-    end
-})
-
-require("jupynvim").setup({
-    log_level = "debug",
-    image_renderer = "placeholder",  -- "placeholder", "kitty", or "chafa"
-})
-
-require("overseer").setup({
-    templates = { "builtin", "user" },
-    component_aliases = {
-        default = {
-            { 'display_duration', detail_level = 2 },
-            'on_output_summarize',
-            'on_exit_set_status',
-            'on_complete_notify',
-            'on_result_diagnostics',
-            {'on_result_diagnostics_quickfix', open = true, close = true},
-        },
-        default_vscode = {
-            'default',
-            'on_result_diagnostics',
-            {'on_result_diagnostics_quickfix', open = true, close = true},
-            'on_complete_notify',
-        },
-    }
-})
-
--- local pm = require("overseer.template.vscode.problem_matcher")
--- pm.register_problem_matcher("$rustc", {
-    --      fileLocation = { "autoDetect", "${cwd}" },
-    --      pattern = {
-        --          --regexp = "^(.*?)-->\\s+(.*?):(\\d+):(\\d+)$",
-        --          -- vim_regexp = "\\v^(.*?)-->\\s+(.*?):(\\d+):(\\d+)$",
-        --          regexp = "^\\s+-->\\s*([^:]*):(\\d+):(\\d+)$",
-        --          vim_regexp = "\\v^\\s+-->\\s*([^:]*):(\\d+):(\\d+)$",
-        --          file = 1,
-        --          line = 2,
-        --          column = 3,
-        --      }
-        -- })
-
-local osys = require("cmake-tools.osys")
-require("cmake-tools").setup {
-    cmake_command = "cmake", -- this is used to specify cmake command path
-    ctest_command = "ctest", -- this is used to specify ctest command path
-    cmake_use_preset = true,
-    cmake_regenerate_on_save = true, -- auto generate when save CMakeLists.txt
-    cmake_generate_options = { "-DCMAKE_EXPORT_COMPILE_COMMANDS=1" }, -- this will be passed when invoke `CMakeGenerate`
-    cmake_build_options = {}, -- this will be passed when invoke `CMakeBuild`
-    -- support macro expansion:
-    --       ${kit}
-    --       ${kitGenerator}
-    --       ${variant:xx}
-    cmake_build_directory = function()
-        if osys.iswin32 then
-            return "out\\${variant:buildType}"
-        end
-        return "out/${variant:buildType}"
-    end, -- this is used to specify generate directory for cmake, allows macro expansion, can be a string or a function returning the string, relative to cwd.
-    cmake_soft_link_compile_commands = true, -- this will automatically make a soft link from compile commands file to project root dir
-    cmake_compile_commands_from_lsp = false, -- this will automatically set compile commands file location using lsp, to use it, please set `cmake_soft_link_compile_commands` to false
-    cmake_kits_path = nil, -- this is used to specify global cmake kits path, see CMakeKits for detailed usage
-    cmake_variants_message = {
-        short = { show = true }, -- whether to show short message
-        long = { show = true, max_length = 40 }, -- whether to show long message
-    },
-    cmake_dap_configuration = { -- debug settings for cmake
-        name = "cpp",
-        type = "codelldb",
-        request = "launch",
-        stopOnEntry = false,
-        runInTerminal = true,
-        console = "integratedTerminal",
-    },
-    cmake_executor = { -- executor to use
-        name = "quickfix", -- name of the executor
-        opts = {}, -- the options the executor will get, possible values depend on the executor type. See `default_opts` for possible values.
-        default_opts = { -- a list of default and possible values for executors
-            quickfix = {
-                show = "always", -- "always", "only_on_error"
-                position = "belowright", -- "vertical", "horizontal", "leftabove", "aboveleft", "rightbelow", "belowright", "topleft", "botright", use `:h vertical` for example to see help on them
-                size = 10,
-                encoding = "utf-8", -- if encoding is not "utf-8", it will be converted to "utf-8" using `vim.fn.iconv`
-                auto_close_when_success = true, -- typically, you can use it with the "always" option; it will auto-close the quickfix buffer if the execution is successful.
-            },
-            toggleterm = {
-                direction = "float", -- 'vertical' | 'horizontal' | 'tab' | 'float'
-                close_on_exit = false, -- whether close the terminal when exit
-                auto_scroll = true, -- whether auto scroll to the bottom
-                singleton = true, -- single instance, autocloses the opened one, if present
-            },
-            overseer = {
-                new_task_opts = {
-                    strategy = {
-                        "toggleterm",
-                        direction = "horizontal",
-                        autos_croll = true,
-                        quit_on_exit = "success"
-                    }
-                }, -- options to pass into the `overseer.new_task` command
-                on_new_task = function(task)
-                    require("overseer").open(
-                        { enter = false, direction = "right" }
-                    )
-                end,   -- a function that gets overseer.Task when it is created, before calling `task:start`
-            },
-            terminal = {
-                name = "Main Terminal",
-                prefix_name = "[CMakeTools]: ", -- This must be included and must be unique, otherwise the terminals will not work. Do not use a simple spacebar " ", or any generic name
-                split_direction = "horizontal", -- "horizontal", "vertical"
-                split_size = 11,
-
-                -- Window handling
-                single_terminal_per_instance = true, -- Single viewport, multiple windows
-                single_terminal_per_tab = true, -- Single viewport per tab
-                keep_terminal_static_location = true, -- Static location of the viewport if avialable
-                auto_resize = true, -- Resize the terminal if it already exists
-
-                -- Running Tasks
-                start_insert = false, -- If you want to enter terminal with :startinsert upon using :CMakeRun
-                focus = false, -- Focus on terminal when cmake task is launched.
-                do_not_add_newline = false, -- Do not hit enter on the command inserted when using :CMakeRun, allowing a chance to review or modify the command before hitting enter.
-            }, -- terminal executor uses the values in cmake_terminal
-        },
-    },
-    cmake_runner = { -- runner to use
-        name = "terminal", -- name of the runner
-        opts = {}, -- the options the runner will get, possible values depend on the runner type. See `default_opts` for possible values.
-        default_opts = { -- a list of default and possible values for runners
-            quickfix = {
-                show = "always", -- "always", "only_on_error"
-                position = "belowright", -- "bottom", "top"
-                size = 10,
-                encoding = "utf-8",
-                auto_close_when_success = true, -- typically, you can use it with the "always" option; it will auto-close the quickfix buffer if the execution is successful.
-            },
-            toggleterm = {
-                direction = "float", -- 'vertical' | 'horizontal' | 'tab' | 'float'
-                close_on_exit = false, -- whether close the terminal when exit
-                auto_scroll = true, -- whether auto scroll to the bottom
-                singleton = true, -- single instance, autocloses the opened one, if present
-            },
-            overseer = {
-                new_task_opts = {
-                    strategy = {
-                        "toggleterm",
-                        direction = "horizontal",
-                        autos_croll = true,
-                        quit_on_exit = "success"
-                    }
-                }, -- options to pass into the `overseer.new_task` command
-                on_new_task = function(task)
-                end,   -- a function that gets overseer.Task when it is created, before calling `task:start`
-            },
-            terminal = {
-                name = "Main Terminal",
-                prefix_name = "[CMakeTools]: ", -- This must be included and must be unique, otherwise the terminals will not work. Do not use a simple spacebar " ", or any generic name
-                split_direction = "horizontal", -- "horizontal", "vertical"
-                split_size = 11,
-
-                -- Window handling
-                single_terminal_per_instance = true, -- Single viewport, multiple windows
-                single_terminal_per_tab = true, -- Single viewport per tab
-                keep_terminal_static_location = true, -- Static location of the viewport if avialable
-                auto_resize = true, -- Resize the terminal if it already exists
-
-                -- Running Tasks
-                start_insert = false, -- If you want to enter terminal with :startinsert upon using :CMakeRun
-                focus = false, -- Focus on terminal when cmake task is launched.
-                do_not_add_newline = false, -- Do not hit enter on the command inserted when using :CMakeRun, allowing a chance to review or modify the command before hitting enter.
-            },
-        },
-    },
-    cmake_notifications = {
-        runner = { enabled = true },
-        executor = { enabled = true },
-        spinner = { "⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏" }, -- icons used for progress display
-        refresh_rate_ms = 100, -- how often to iterate icons
-    },
-    cmake_virtual_text_support = true, -- Show the target related to current file using virtual text (at right corner)
-}
-
-vim.keymap.set({'n'}, '<leader>vn', '<cmd>Neogit kind=auto<cr>', { desc = 'Neogit' })
-vim.keymap.set({'n'}, '<leader>vN', '<cmd>Neogit kind=floating<cr>', { desc = 'Neogit' })
-
 vim.keymap.set({'n'}, '<leader>kp', '<cmd>PasteImage<cr>', { desc = "Paste image from system clipboard"  })
-vim.keymap.set({'n'}, '<leader>xM', '<cmd>Lazy reload mise.nvim<cr>', { desc = "Reload mise environment"  })
-vim.keymap.set({'n'}, '<leader>uu', vim.cmd.UndotreeToggle, { desc = 'Undo Tree toggle' })
 
-vim.keymap.set('n', "<leader>cx", "<cmd>Trouble diagnostics toggle<cr>", { desc = "Diagnostics (Trouble)" })
-vim.keymap.set('n', "<leader>cX", "<cmd>Trouble diagnostics toggle filter.buf=0<cr>", { desc = "Buffer Diagnostics (Trouble)" })
-vim.keymap.set('n', "<leader>cs", "<cmd>Trouble symbols toggle focus=false<cr>", { desc = "Symbols (Trouble)" })
-vim.keymap.set('n', "<leader>cl", "<cmd>Trouble lsp toggle focus=false win.position=right<cr>", { desc = "LSP Definitions / references / ... (Trouble)" })
-vim.keymap.set('n', "<leader>cL", "<cmd>Trouble loclist toggle<cr>", { desc = "Location List (Trouble)" })
-vim.keymap.set('n', "<leader>cQ", "<cmd>Trouble qflist toggle<cr>", { desc = "Quickfix List (Trouble)" })
-
-vim.keymap.set('n', "<leader>uo", "<cmd>OverseerToggle<CR>", { desc = "Overseer Toggle"  })
-vim.keymap.set('n', "<F5>", "<cmd>OverseerRun<CR>", { desc = "Run Overseer"  })
-vim.keymap.set('n', "<F6>", "<cmd>OverseerToggle<CR>", { desc = "Overseer Toggle"  })

config/nvim/plugin/treesitter.lua

@@ -1,3 +1,12 @@
+vim.pack.add({
+    { src = 'https://github.com/nvim-treesitter/nvim-treesitter', version = 'main' },
+    { src = 'https://github.com/nvim-treesitter/nvim-treesitter-context' },
+    { src = 'https://github.com/nvim-treesitter/nvim-treesitter-context' },
+    { src = 'https://github.com/nvim-treesitter/nvim-treesitter-textobjects', version = 'main' },
+    { src = 'https://github.com/romus204/tree-sitter-manager.nvim' },
+    { src = 'https://github.com/JoosepAlviste/nvim-ts-context-commentstring' },
+})
+
 require("tree-sitter-manager").setup({
     -- Default Options
     -- ensure_installed = {}, -- list of parsers to install at the start of a neovim session

config/nvim/plugin/trouble.lua

@@ -0,0 +1,18 @@
+vim.pack.add({
+    { src = "https://github.com/folke/trouble.nvim" },
+})
+
+require('trouble').setup({
+    defaults = {
+        auto_close = true,
+        auto_open = true,
+    },
+})
+
+vim.keymap.set('n', "<leader>cx", "<cmd>Trouble diagnostics toggle<cr>", { desc = "Diagnostics (Trouble)" })
+vim.keymap.set('n', "<leader>cX", "<cmd>Trouble diagnostics toggle filter.buf=0<cr>", { desc = "Buffer Diagnostics (Trouble)" })
+vim.keymap.set('n', "<leader>cs", "<cmd>Trouble symbols toggle focus=false<cr>", { desc = "Symbols (Trouble)" })
+vim.keymap.set('n', "<leader>cl", "<cmd>Trouble lsp toggle focus=false win.position=right<cr>", { desc = "LSP Definitions / references / ... (Trouble)" })
+vim.keymap.set('n', "<leader>cL", "<cmd>Trouble loclist toggle<cr>", { desc = "Location List (Trouble)" })
+vim.keymap.set('n', "<leader>cQ", "<cmd>Trouble qflist toggle<cr>", { desc = "Quickfix List (Trouble)" })
+

config/nvim/plugin/undotree.lua

@@ -0,0 +1,5 @@
+vim.pack.add({
+    { src = 'https://github.com/mbbill/undotree' },
+})
+
+vim.keymap.set({'n'}, '<leader>uu', vim.cmd.UndotreeToggle, { desc = 'Undo Tree toggle' })

config/nvim/plugin/vim-tmux-navigator.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/christoomey/vim-tmux-navigator' },
+})
+
 vim.keymap.set('n', "<c-h>", "<cmd><C-U>TmuxNavigateLeft<cr>" )
 vim.keymap.set('n', "<c-j>", "<cmd><C-U>TmuxNavigateDown<cr>" )
 vim.keymap.set('n', "<c-k>", "<cmd><C-U>TmuxNavigateUp<cr>" )

config/nvim/plugin/vimtex.lua

@@ -1,3 +1,6 @@
+vim.pack.add({
+    { src = 'https://github.com/lervag/vimtex' },
+})
 vim.g.tex_flavor = "latex"
 vim.g.vimtex_view_method = "zathura" -- Change to your preferred PDF viewer
 vim.g.vimtex_quickfix_mode = 0       -- Disable quickfix window

config/nvim/plugin/which-key.lua

@@ -1,3 +1,7 @@
+vim.pack.add({
+    { src = 'https://github.com/folke/which-key.nvim' },
+})
+
 require('which-key').setup({
     icons = {
         -- set icon mappings to true if you have a Nerd Font

config/nvim/plugin/window-picker.lua

@@ -1,3 +1,6 @@
+vim.pack.add({
+    { src = 'https://github.com/ten3roberts/window-picker.nvim' },
+})
 
 require('window-picker').setup({
     -- Default keys to annotate, keys will be used in order. The default uses the

config/nvim/plugin/zoxide.lua

@@ -0,0 +1,11 @@
+if vim.fn.executable("zoxide") == 1 then
+    vim.pack.add({
+        { src = 'https://github.com/thunder-coding/zincoxide' },
+    })
+    require('zincoxide').setup({
+        zincoxide_cmd = "zoxide",
+        complete = true,
+        behaviour = "tabs",
+    })
+end
+