nvim: Make utility terminals dockable and hidable

The utility terminals (lazygit and python repl for now) can now be hidden
even from terminal insert mode (i.e. when interacting with them) with
<C-\>. They can be invoked through their usual chords (<leader>tg and
<leader>tp respectively) again and will pick right up where you left off.

Insert mode in terminals can also be left slightly easier should it
be needed: Instead of the <C-\><C-n> chord you can use j\.

Lastly, the utility terminals can be started in a vertically docked mode
instead of floating. This is done by adding a bang to their commands,
`Lazygit!` and `Pythonterm!`, or using capital versions of their
mappings: <leader>tG and <leader>tP.

desktop/.config/user-dirs.dirs

@@ -0,0 +1,15 @@
+# This file is written by xdg-user-dirs-update
+# If you want to change or add directories, just edit the line you're
+# interested in. All local changes will be retained on the next run.
+# Format is XDG_xxx_DIR="$HOME/yyy", where yyy is a shell-escaped
+# homedir-relative path, or XDG_xxx_DIR="/yyy", where /yyy is an
+# absolute path. No other format is supported.
+# 
+XDG_DESKTOP_DIR="$HOME/desktop"
+XDG_DOCUMENTS_DIR="$HOME/documents"
+XDG_DOWNLOAD_DIR="$HOME/downloads"
+XDG_MUSIC_DIR="$HOME/media/audio/music"
+XDG_PICTURES_DIR="$HOME/pictures"
+XDG_PUBLICSHARE_DIR="$HOME/"
+XDG_TEMPLATES_DIR="$HOME/"
+XDG_VIDEOS_DIR="$HOME/"

nvim/.config/nvim/init.lua

@@ -4,31 +4,19 @@ local api = vim.api
 
 api.nvim_exec2("runtime abbrev.vim", {})
 
-local lazypath = vim.fn.stdpath("data") .. "/lazy/lazy.nvim"
-if not vim.loop.fs_stat(lazypath) then
-	vim.fn.system({
-		"git",
-		"clone",
-		"--filter=blob:none",
-		"https://github.com/folke/lazy.nvim.git",
-		"--branch=stable", -- latest stable release
-		lazypath,
-	})
+for _, source in ipairs({
+	"core.settings",
+	"core.lazy",
+	"core.autocmds",
+	"core.mappings",
+	"core.look",
+	"personal",
+}) do
+	local status_ok, fault = pcall(require, source)
+	if not status_ok then
+		vim.api.nvim_err_writeln("Failed to load " .. source .. "\n\n" .. fault)
+	end
 end
-vim.opt.rtp:prepend(lazypath)
-
--- set our leader key to space since with hjkl, space is largely useless
--- needs to be set before lazy.nvim is loaded
-vim.g.mapleader = " "
-
-require("settings")
-require("autocmds")
-require("lazy").setup("plugins", {
-	defaults = { version = "*" },
-	performance = { rtp = { disabled_plugins = { "netrw", "netrwPlugin" } } },
-})
-require("look")
-require("maps")
 
 -- to include e.g. the spell dictionaries for vim
 vim.opt.rtp:append(vim.fn.stdpath("data") .. "/site")

nvim/.config/nvim/lazy-lock.json

@@ -7,7 +7,7 @@
   "cmp-beancount": { "branch": "main", "commit": "da154ea94d598e6649d6ad01efa0a8611eff460d" },
   "cmp-buffer": { "branch": "main", "commit": "3022dbc9166796b644a841a02de8dd1cc1d311fa" },
   "cmp-calc": { "branch": "main", "commit": "50792f34a628ea6eb31d2c90e8df174671e4e7a0" },
-  "cmp-cmdline": { "branch": "main", "commit": "5af1bb7d722ef8a96658f01d6eb219c4cf746b32" },
+  "cmp-cmdline": { "branch": "main", "commit": "8ee981b4a91f536f52add291594e89fb6645e451" },
   "cmp-digraphs": { "branch": "master", "commit": "5efc1f0078d7c5f3ea1c8e3aad04da3fd6e081a9" },
   "cmp-latex-symbols": { "branch": "main", "commit": "165fb66afdbd016eaa1570e41672c4c557b57124" },
   "cmp-nvim-lsp": { "branch": "main", "commit": "0e6b2ed705ddcff9738ec4ea838141654f12eeef" },
@@ -24,36 +24,35 @@
   "dressing.nvim": { "branch": "master", "commit": "f16d7586fcdd8b2e3850d0abb7e46f944125cc25" },
   "easyread.nvim": { "branch": "main", "commit": "0b07e315a4cd7d700c4a794bdddbec79fdc2628b" },
   "fidget.nvim": { "branch": "main", "commit": "0ba1e16d07627532b6cae915cc992ecac249fb97" },
-  "friendly-snippets": { "branch": "main", "commit": "b471f5419155ce832eff71ad8920ea8cfbd54840" },
+  "friendly-snippets": { "branch": "main", "commit": "b3cd8d77feb7871d8b04bb45bcd8154120a796a1" },
   "fwatch.nvim": { "branch": "main", "commit": "a691f7349dc66285cd75a1a698dd28bca45f2bf8" },
   "gitsigns.nvim": { "branch": "main", "commit": "bb808fc7376ed7bac0fbe8f47b83d4bf01738167" },
   "jupyter-kernel.nvim": { "branch": "main", "commit": "5b409598033884a3d819e2a3bcd1fe340bc8d783" },
-  "lazy.nvim": { "branch": "main", "commit": "f145e6f42a56306c5536e9efbfe41f7efbec285d" },
+  "lazy.nvim": { "branch": "main", "commit": "6b2311a46a3808e366bb251270f4cc04afb421ed" },
   "lightspeed.nvim": { "branch": "main", "commit": "299eefa6a9e2d881f1194587c573dad619fdb96f" },
-  "lsp-zero.nvim": { "branch": "v2.x", "commit": "8fda9a849d6ab4196ecf129905764ddefdfb64b5" },
+  "lsp-setup.nvim": { "branch": "main", "commit": "4656a1882546b702b18a84f5de209a2f8aa43dee" },
   "lsp_signature.nvim": { "branch": "master", "commit": "4665921ff8e30601c7c1328625b3abc1427a6143" },
   "lualine.nvim": { "branch": "master", "commit": "05d78e9fd0cdfb4545974a5aa14b1be95a86e9c9" },
-  "magma-nvim-goose": { "branch": "main", "commit": "5d916c39c1852e09fcd39eab174b8e5bbdb25f8f" },
+  "magma-nvim-goose": { "branch": "main", "commit": "d7931d773efcedc9c92337b8d500e32a3725fe26" },
   "markdown-preview.nvim": { "branch": "master", "commit": "9becceee5740b7db6914da87358a183ad11b2049" },
   "mason-lspconfig.nvim": { "branch": "main", "commit": "5230617372e656d4a2e1e236e03bf7e7b4b97273" },
   "mason-null-ls.nvim": { "branch": "main", "commit": "cfbd83909cbc56e2f07cb3f8a03157e069c5c91c" },
-  "mason.nvim": { "branch": "main", "commit": "7d7efc738e08fc5bee822857db45cb6103f0b0c1" },
-  "mini.nvim": { "branch": "main", "commit": "889be69623395ad183ae6f3c21c8efe006350226" },
+  "mason.nvim": { "branch": "main", "commit": "4be1226f48bc2011024110f37b17f5ee468df58f" },
+  "mini.nvim": { "branch": "main", "commit": "296ebbbd3e5ba5e43f5125efe18ad76fe3b632cc" },
   "nabla.nvim": { "branch": "master", "commit": "8c143ad2b3ab3b8ffbd51e238ccfcbd246452a7e" },
-  "neural": { "branch": "main", "commit": "155618730b87a67655bdde373ee27bfce8b07ac9" },
-  "nui.nvim": { "branch": "main", "commit": "7a524120a7a70761b5a65b602fd235a65cb005aa" },
   "null-ls.nvim": { "branch": "main", "commit": "a138b14099e9623832027ea12b4631ddd2a49256" },
   "nvim-base16": { "branch": "master", "commit": "4f3aa29f49b38edb6db1c52cea57e64ce3de2373" },
-  "nvim-cmp": { "branch": "main", "commit": "fc0f694af1a742ada77e5b1c91ff405c746f4a26" },
+  "nvim-cmp": { "branch": "main", "commit": "b8c2a62b3bd3827aa059b43be3dd4b5c45037d65" },
   "nvim-colorizer.lua": { "branch": "master", "commit": "dde3084106a70b9a79d48f426f6d6fec6fd203f7" },
-  "nvim-lspconfig": { "branch": "master", "commit": "458fa2ee2115c693ca48a04afa65f6de6b40a2db" },
+  "nvim-lspconfig": { "branch": "master", "commit": "295c646488d5baa63c6c4da68fe61171b9257375" },
   "nvim-notify": { "branch": "master", "commit": "ea9c8ce7a37f2238f934e087c255758659948e0f" },
   "nvim-surround": { "branch": "main", "commit": "211eaad7c6d01ef4ac02cba9052b3082ec232101" },
   "nvim-toggleterm.lua": { "branch": "main", "commit": "95204ece0f2a54c89c4395295432f9aeedca7b5f" },
-  "nvim-tree.lua": { "branch": "master", "commit": "f5d970d4506f385b29534252d8c15a782fa53034" },
+  "nvim-tree.lua": { "branch": "master", "commit": "f873625d0636889af4cd47a01e486beb865db205" },
   "nvim-treesitter": { "branch": "master", "commit": "cc360a9beb1b30d172438f640e2c3450358c4086" },
-  "nvim-treesitter-context": { "branch": "master", "commit": "e2ea37627c0681421ccf4a3cf19d68bb958e1817" },
+  "nvim-treesitter-context": { "branch": "master", "commit": "efe87061af560847679fca93697991e474f049e2" },
   "nvim-treesitter-textsubjects": { "branch": "master", "commit": "b913508f503527ff540f7fe2dcf1bf1d1f259887" },
+  "nvim-ts-autotag": { "branch": "main", "commit": "e254b306fb81ed69049cce526e7906150d73e0d1" },
   "nvim-ts-context-commentstring": { "branch": "main", "commit": "0bf8fbc2ca8f8cdb6efbd0a9e32740d7a991e4c3" },
   "nvim-ts-rainbow2": { "branch": "master", "commit": "c00d61ab7517530c49457ba49186776e6611a3e1" },
   "nvim-web-devicons": { "branch": "master", "commit": "2a125024a137677930efcfdf720f205504c97268" },
@@ -62,12 +61,12 @@
   "plenary.nvim": { "branch": "master", "commit": "253d34830709d690f013daf2853a9d21ad7accab" },
   "popup.nvim": { "branch": "master", "commit": "b7404d35d5d3548a82149238289fa71f7f6de4ac" },
   "quarto-nvim": { "branch": "main", "commit": "b299266c6287d74b60480fae348d629ec1dc02bb" },
-  "significant.nvim": { "branch": "main", "commit": "5450e9d5917dc6aa9afb0fcbe32355799b8303fb" },
   "smartcolumn.nvim": { "branch": "main", "commit": "0c572e3eae48874f25b74394a486f38cadb5c958" },
   "symbols-outline.nvim": { "branch": "master", "commit": "512791925d57a61c545bc303356e8a8f7869763c" },
   "telescope-fzf-native.nvim": { "branch": "main", "commit": "9bc8237565ded606e6c366a71c64c0af25cd7a50" },
-  "telescope.nvim": { "branch": "master", "commit": "c1a2af0af69e80e14e6b226d3957a064cd080805" },
+  "telescope.nvim": { "branch": "master", "commit": "776b509f80dd49d8205b9b0d94485568236d1192" },
   "twilight.nvim": { "branch": "main", "commit": "8bb7fa7b918baab1ca81b977102ddb54afa63512" },
+  "undotree": { "branch": "main", "commit": "2685ce282702ab0b79c65916f352db2265b245dd" },
   "vifm.vim": { "branch": "master", "commit": "a8130c37d144b51d84bee19f0532abcd3583383f" },
   "vim-criticmarkup": { "branch": "master", "commit": "d15dc134eb177a170c79f6377f81eb02a9d20b02" },
   "vim-easy-align": { "branch": "master", "commit": "0db4ea6132110631ec678a99a82aa49a0686ae65" },

nvim/.config/nvim/lua/autocmds.lua

@@ -1,37 +0,0 @@
--- Highlight whatever is being yanked
-vim.api.nvim_create_autocmd({ "TextYankPost" }, {
-	command = 'silent! lua require"vim.highlight".on_yank{timeout=500}',
-	desc = "Highlight yanked text whenevery yanking something",
-	group = vim.api.nvim_create_augroup("highlightyanks", { clear = true }),
-})
-
--- Special setting for editing gopass files - make sure nothing leaks outside the directories it is supposed to
-vim.api.nvim_create_autocmd({ "BufNewFile", "BufRead" }, {
-	pattern = {
-		"/dev/shm/gopass.*",
-		"/dev/shm/pass.?*/?*.txt",
-		"$TMPDIR/pass.?*/?*.txt",
-		"/tmp/pass.?*/?*.txt",
-	},
-	command = "setlocal noswapfile nobackup noundofile nowritebackup viminfo=",
-	desc = "Don't leak any information when editing potential password files",
-	group = vim.api.nvim_create_augroup("passnoleak", { clear = true }),
-})
-
--- fixing neovim opening up at same moment as alacritty (see https://github.com/neovim/neovim/issues/11330)
-vim.api.nvim_create_autocmd({ "VimEnter" }, {
-	callback = function()
-		local pid, WINCH = vim.fn.getpid(), vim.loop.constants.SIGWINCH
-		vim.defer_fn(function()
-			vim.loop.kill(pid, WINCH)
-		end, 20)
-	end,
-	desc = "Fix neovim sizing issues if opening same time as alacritty",
-	group = vim.api.nvim_create_augroup("alacritty_fixsize", { clear = true }),
-})
-
--- remove line numbers from terminal buffers
-vim.api.nvim_create_autocmd({ "TermOpen" }, {
-	pattern = "*",
-	command = "setlocal nonumber norelativenumber",
-})

nvim/.config/nvim/lua/core/autocmds.lua

@@ -0,0 +1,38 @@
+-- Highlight whatever is being yanked
+vim.api.nvim_create_autocmd({ "TextYankPost" }, {
+    command = 'silent! lua require"vim.highlight".on_yank{timeout=500}',
+    desc = "Highlight yanked text whenevery yanking something",
+    group = vim.api.nvim_create_augroup("highlightyanks", { clear = true }),
+})
+
+-- Special setting for editing gopass files - make sure nothing leaks outside the directories it is supposed to
+vim.api.nvim_create_autocmd({ "BufNewFile", "BufRead" }, {
+    pattern = {
+        "/dev/shm/gopass.*",
+        "/dev/shm/pass.?*/?*.txt",
+        "$TMPDIR/pass.?*/?*.txt",
+        "/tmp/pass.?*/?*.txt",
+    },
+    command = "setlocal noswapfile nobackup noundofile nowritebackup viminfo=",
+    desc = "Don't leak any information when editing potential password files",
+    group = vim.api.nvim_create_augroup("passnoleak", { clear = true }),
+})
+
+-- fixing neovim opening up at same moment as alacritty (see https://github.com/neovim/neovim/issues/11330)
+vim.api.nvim_create_autocmd({ "VimEnter" }, {
+    callback = function()
+        local pid, WINCH = vim.fn.getpid(), vim.loop.constants.SIGWINCH
+        vim.defer_fn(function()
+            vim.loop.kill(pid, WINCH)
+        end, 20)
+    end,
+    desc = "Fix neovim sizing issues if opening same time as alacritty",
+    group = vim.api.nvim_create_augroup("alacritty_fixsize", { clear = true }),
+})
+
+-- remove line numbers from terminal buffers
+vim.api.nvim_create_autocmd({ "TermOpen" }, {
+    desc = "Hide buffer numbers for terminals",
+    pattern = "*",
+    command = "setlocal nonumber norelativenumber",
+})

nvim/.config/nvim/lua/core/lazy.lua

@@ -0,0 +1,38 @@
+local lazypath = vim.fn.stdpath("data") .. "/lazy/lazy.nvim"
+-- inspired from astronvim lazy bootstrapping
+if not vim.loop.fs_stat(lazypath) then
+	local output = vim.fn.system({
+		"git",
+		"clone",
+		"--filter=blob:none",
+		"https://github.com/folke/lazy.nvim.git",
+		"--branch=stable",
+		lazypath,
+	})
+	if vim.api.nvim_get_vvar("shell_error") ~= 0 then
+		vim.api.nvim_err_writeln("Error cloning lazy.nvim repository...\n\n" .. output)
+	end
+	local oldcmdheight = vim.opt.cmdheight:get()
+	vim.opt.cmdheight = 1
+	vim.notify("Please wait while plugins are installed...")
+	vim.api.nvim_create_autocmd("User", {
+		desc = "Load Mason and Treesitter after Lazy installs plugins",
+		once = true,
+		pattern = "LazyInstall",
+		callback = function()
+			vim.cmd.bw()
+			vim.opt.cmdheight = oldcmdheight
+			vim.tbl_map(function(module)
+				pcall(require, module)
+			end, { "nvim-treesitter", "mason" })
+			vim.notify("Mason is installing packages if configured, check status with :Mason")
+		end,
+	})
+end
+vim.opt.rtp:prepend(lazypath)
+
+require("lazy").setup({
+	spec = { { import = "plugins" } },
+	defaults = { lazy = true, version = "*" },
+	performance = { rtp = { disabled_plugins = { "netrw", "netrwPlugin" } } },
+})

nvim/.config/nvim/lua/core/mappings.lua

@@ -1,5 +1,6 @@
 local map = vim.keymap.set
 local prefix = require("which-key").register
+local is_available = require("util").is_available
 
 -- The general ideas behind these mappings:
 --
@@ -95,6 +96,9 @@ if vim.g.maplocalleader == "," then
 	vim.keymap.del("", ",,", { silent = true })
 end
 
+-- get out of terminal mode a little easier by double tapping backslash
+map("t", "\\\\", [[<C-\><C-n>]], { desc = "exit terminal mode" })
+
 -- remove search highlights by pressing space+/
 map("n", "<leader>/", ":noh<cr>", { desc = "remove highlights" })
 
@@ -102,8 +106,6 @@ map("n", "<leader>/", ":noh<cr>", { desc = "remove highlights" })
 -- tmux setup)
 map("n", "<leader>-", ":sp<cr>", { desc = "open horiz split" })
 map("n", "<leader>\\", ":vsp<cr>", { desc = "open vert split" })
--- 'open new buffer' with leader-t (opens new buffer containing current dir and switches to it)
-map("n", "<leader>t", ":vsp | Vifm<cr>", { desc = "open buffer" })
 -- open actual new tab with leader-T
 map("n", "<leader>T", ":tabedit | Vifm<cr>", { desc = "open tab" })
 
@@ -251,8 +253,15 @@ map("v", "<localleader>nN", ":ZkNewFromContentSelection<cr>", { desc = "content
 map("v", "<localleader>nf", ":ZkMatch<cr>", { desc = "find note from selection" })
 
 -- PLUGIN: toggleterm.nvim
--- create a lazygit window, set up in toggleterm settings
+-- create a lazygit or python window, set up in toggleterm settings
+-- TODO create ability to go into python environment when in poetry venv and/or euporie/jupyter notebook
+if is_available("nvim-toggleterm.lua") then
 	map("n", "<leader>G", ":Lazygit<cr>")
+	map("n", "<leader>tg", ":Lazygit<cr>")
+	map("n", "<leader>tG", ":Lazygit!<cr>")
+	map("n", "<leader>tp", ":Pythonterm<cr>")
+	map("n", "<leader>tP", ":Pythonterm!<cr>")
+end
 
 prefix({ ["<localleader>s"] = { name = "+set" } })
 -- PLUGIN: wrapping.nvim
@@ -280,3 +289,10 @@ map(
 	'<cmd>lua require("colorizer").attach_to_buffer(0, {mode = "background"} )<cr>',
 	{ silent = true, desc = "colorize background" }
 )
+
+-- PLUGIN: undotree
+if is_available("undotree") then
+	map("n", "<leader>su", function()
+		require("undotree").toggle()
+	end, { silent = true, desc = "toggle undotree" })
+end

nvim/.config/nvim/lua/core/settings.lua

@@ -4,8 +4,13 @@ local disable_builtins = function(builtins)
 		vim.g["loaded_" .. plugin] = 1
 	end
 end
+disable_builtins(default_builtins_disabled)
 
-local o = {
+if vim.fn.has("nvim-0.9") == 1 then
+	vim.opt.diffopt:append("linematch:60")
+end
+
+local options = {
 	termguicolors = true,
 	-- sets tabs to be 2 characters, expanded into spaces, but still removable with
 	-- one press of backspace.
@@ -47,6 +52,7 @@ local o = {
 	-- set to use treesitter in treesitter config
 	foldlevel = 2,
 	conceallevel = 2,
+	foldcolumn = vim.fn.has("nvim-0.9") == 1 and "auto:1" or nil,
 	-- enable mouse, doesn't bug me and might come in useful at some point
 	mouse = "a",
 	-- pump all clippings into the system clipboard
@@ -60,11 +66,27 @@ local o = {
 	splitbelow = true,
 	-- remove command line if no command is currently present
 	cmdheight = 0,
+	-- try to cleverly manage indents by preserving them from line to line
+	breakindent = true,
+	copyindent = true,
+	preserveindent = true,
+	smartindent = true,
 }
 
-for k, v in pairs(o) do
-	vim.opt[k] = v
+for o, v in pairs(options) do
+	vim.opt[o] = v
 end
+vim.opt.shortmess:append({ s = true, I = true })
+vim.opt.backspace:append({ "nostop" })
 
-vim.api.nvim_set_var("tex_flavor", "latex")
-disable_builtins(default_builtins_disabled)
+local globals = {
+	mapleader = " ",
+	maplocalleader = ",",
+	tex_flavor = "latex",
+
+	format_on_save = true, -- from personal toggle function
+}
+
+for o, v in pairs(globals) do
+	vim.g[o] = v
+end

nvim/.config/nvim/lua/personal/format_on_save_toggle.lua

@@ -0,0 +1,33 @@
+local function stop_formatting()
+	vim.api.nvim_del_augroup_by_name("LspFormat")
+end
+
+local function start_formatting()
+	for _, client in pairs(vim.lsp.get_active_clients()) do
+		require("lsp-setup.utils").format_on_save(client)
+	end
+end
+
+local function _toggle(opts)
+	if opts.args == "" then
+		vim.g.format_on_save = not vim.g.format_on_save
+	elseif opts.args == "on" or opts.args == "1" then
+		vim.g.format_on_save = true
+	elseif opts.args == "off" or opts.args == "0" then
+		vim.g.format_on_save = false
+	else
+		vim.notify("Please provide arguments 'on' or 'off' or non arguments to toggle.")
+	end
+
+	if vim.g.format_on_save == true then
+		start_formatting()
+	else
+		stop_formatting()
+	end
+end
+
+vim.api.nvim_create_user_command(
+	"FormatOnSave",
+	_toggle,
+	{ desc = "toggle automatically formatting on save", nargs = "?" }
+)

nvim/.config/nvim/lua/personal/init.lua

@@ -0,0 +1 @@
+require("personal.format_on_save_toggle")

nvim/.config/nvim/lua/personal/pandoc_complete.lua

@@ -1,11 +0,0 @@
-local M = {}
-
-function M.getCompletionItems(prefix)
-	-- define your total completion items
-	local items = vim.api.nvim_call_function("pandoc#completion#Complete", { 0, prefix })
-	return items
-end
-
-M.complete_item = { item = M.getCompletionItems }
-
-return M

nvim/.config/nvim/lua/plug/_gitsigns.lua

@@ -1,56 +0,0 @@
-require("gitsigns").setup({
-	numhl = true,
-	signcolumn = false,
-	on_attach = function(bufnr)
-		local gs = package.loaded.gitsigns
-
-		local function map(mode, l, r, opts)
-			opts = opts or {}
-			opts.buffer = bufnr
-			vim.keymap.set(mode, l, r, opts)
-		end
-
-		-- Navigation
-		map("n", "]h", function()
-			if vim.wo.diff then
-				return "]h"
-			end
-			vim.schedule(function()
-				gs.next_hunk()
-			end)
-			return "<Ignore>"
-		end, { expr = true })
-
-		map("n", "[h", function()
-			if vim.wo.diff then
-				return "[h"
-			end
-			vim.schedule(function()
-				gs.prev_hunk()
-			end)
-			return "<Ignore>"
-		end, { expr = true })
-
-		-- Actions
-		require("which-key").register({ ["<localleader>h"] = { name = "+git" } })
-		map({ "n", "v" }, "<localleader>hs", ":Gitsigns stage_hunk<CR>", { desc = "stage hunk" })
-		map({ "n", "v" }, "<localleader>hr", ":Gitsigns reset_hunk<CR>", { desc = "reset hunk" })
-		map("n", "<localleader>hS", gs.stage_buffer, { desc = "stage buffer" })
-		map("n", "<localleader>hu", gs.undo_stage_hunk, { desc = "undo stage hunk" })
-		map("n", "<localleader>hR", gs.reset_buffer, { desc = "reset buffer" })
-		map("n", "<localleader>hp", gs.preview_hunk, { desc = "preview hunk" })
-		map("n", "<localleader>hb", function()
-			gs.blame_line({ full = true })
-		end, { desc = "blame line" })
-		map("n", "<localleader>hB", gs.toggle_current_line_blame, { desc = "toggle blame" })
-		map("n", "<localleader>hd", gs.diffthis, { desc = "diffthis" })
-		map("n", "<localleader>hD", function()
-			gs.diffthis("~")
-		end, { desc = "diffbase" })
-		map("n", "<localleader>ht", gs.toggle_deleted, { desc = "toggle deleted" })
-
-		-- Text object
-		map({ "o", "x" }, "ih", ":<C-U>Gitsigns select_hunk<CR>")
-		map({ "o", "x" }, "ah", ":<C-U>Gitsigns select_hunk<CR>")
-	end,
-})

nvim/.config/nvim/lua/plug/_lsp.lua

@@ -1,329 +0,0 @@
-local lsp = require("lsp-zero")
-
-vim.diagnostic.config({ virtual_text = true })
-vim.fn.sign_define("DiagnosticSignError", { text = "✘", texthl = "DiagnosticSignError" })
-vim.fn.sign_define("DiagnosticSignWarn", { text = "", texthl = "DiagnosticSignWarn" })
-vim.fn.sign_define("DiagnosticSignInfo", { text = "", texthl = "DiagnosticSignInfo" })
-vim.fn.sign_define("DiagnosticSignHint", { text = "", texthl = "DiagnosticSignHint" })
-
-lsp.ensure_installed({
-	"astro",
-	"arduino_language_server",
-	"bashls",
-	"beancount",
-	"clangd",
-	"dockerls",
-	"docker_compose_language_service",
-	"lua_ls",
-	"pyright",
-	"ruff_lsp",
-	"taplo",
-	"yamlls",
-	"tsserver",
-	"cssls",
-	"tailwindcss",
-})
-lsp.preset({ name = "recommended", set_lsp_keymaps = false })
-lsp.on_attach(function(client, bufnr)
-	local map = vim.keymap.set
-	map("n", "[d", "<cmd>lua vim.diagnostic.goto_prev()<cr>", { buffer = bufnr, desc = "Previous diagnostic" })
-	map("n", "]d", "<cmd>lua vim.diagnostic.goto_next()<cr>", { buffer = bufnr, desc = "Next diagnostic" })
-	map(
-		"n",
-		"[e",
-		"<cmd>lua vim.diagnostic.goto_prev({severity = vim.diagnostic.severity.ERROR})<cr>",
-		{ buffer = bufnr, desc = "Previous error" }
-	)
-	map(
-		"n",
-		"]e",
-		"<cmd>lua vim.diagnostic.goto_next({severity = vim.diagnostic.severity.ERROR})<cr>",
-		{ buffer = bufnr, desc = "Next error" }
-	)
-
-	local prefix = require("which-key").register
-	prefix({ ["<localleader>l"] = { name = "+lsp" } })
-	map("n", "<localleader>li", "<cmd>LspInfo<cr>", { buffer = bufnr, desc = "Lsp Info" })
-	map(
-		"n",
-		"<localleader>ld",
-		"<cmd>lua vim.diagnostic.open_float()<cr>",
-		{ buffer = bufnr, desc = "Line diagnostics" }
-	)
-	map("n", "<localleader>la", "<cmd>lua vim.lsp.buf.code_action()<cr>", { buffer = bufnr, desc = "Codeactions" })
-	map("n", "<localleader>ln", "<cmd>lua vim.lsp.buf.rename()<cr>", { buffer = bufnr, desc = "Rename element" })
-	if vim.fn.exists(":Telescope") then
-		map("n", "<localleader>lr", "<cmd>Telescope lsp_references()<cr>", { buffer = bufnr, desc = "References" })
-		map("n", "<localleader>lf", "<cmd>Telescope lsp_definitions<cr>", { buffer = bufnr, desc = "Definition" })
-		map(
-			"n",
-			"<localleader>lt",
-			"<cmd>Telescope lsp_type_definitions<cr>",
-			{ buffer = bufnr, desc = "Type definition" }
-		)
-		map(
-			"n",
-			"<localleader>lm",
-			"<cmd>Telescope lsp_implementations<cr>",
-			{ buffer = bufnr, desc = "Implementation" }
-		)
-	else
-		map("n", "<localleader>lr", "<cmd>lua vim.lsp.buf.references()<cr>", { buffer = bufnr, desc = "References" })
-		map("n", "<localleader>lf", "<cmd>lua vim.lsp.buf.definition()<cr>", { buffer = bufnr, desc = "Definition" })
-		map(
-			"n",
-			"<localleader>lt",
-			"<cmd>lua vim.lsp.buf.type_definition()<cr>",
-			{ buffer = bufnr, desc = "Type definition" }
-		)
-		map(
-			"n",
-			"<localleader>lm",
-			"<cmd>lua vim.lsp.buf.implementation()<cr>",
-			{ buffer = bufnr, desc = "Implementation" }
-		)
-	end
-	if client.server_capabilities.document_formatting then
-		map(
-			"n",
-			"<localleader>lf",
-			"<cmd>lua vim.lsp.buf.formatting()<CR>",
-			{ buffer = bufnr, desc = "Format document" }
-		)
-	end
-
-	map("n", "K", "<cmd>lua vim.lsp.buf.hover()<cr>", { buffer = bufnr, desc = "Hover definition" })
-	map("n", "<localleader>lc", "<cmd>lua vim.lsp.buf.declaration()<cr>", { buffer = bufnr, desc = "Declaration" })
-	map(
-		"n",
-		"<localleader>ls",
-		"<cmd>lua vim.lsp.buf.signature_help()<cr>",
-		{ buffer = bufnr, desc = "Signature help" }
-	)
-end)
-lsp.nvim_workspace()
--- ensure python virtualenv is determined automatically on lsp start
-require("lspconfig").pyright.setup({
-	on_attach = function(client, _)
-		local python_path, msg = require("util.pyenv").get_path(client.config.root_dir)
-		vim.notify(string.format("%s\n%s", msg, python_path))
-		client.config.settings.python.pythonPath = python_path
-	end,
-})
--- set up arduino with the help of arduino.nvim plugin
-require("lspconfig").arduino_language_server.setup({
-	on_new_config = require("arduino").on_new_config,
-})
-require("lspconfig").lua_ls.setup(lsp.nvim_lua_ls())
-
--- map filetypes (rhs) to individual servers (lhs)
--- most will presumably use null_ls however
-local format_servers = {
-	["null-ls"] = {
-		"astro",
-		"javascript",
-		"javascriptreact",
-		"typescript",
-		"typescriptreact",
-		"vue",
-		"css",
-		"scss",
-		"less",
-		"html",
-		"json",
-		"jsonc",
-		"yaml",
-		"markdown",
-		"markdown.mdx",
-		"graphql",
-		"handlebars",
-		"python",
-		"sh",
-		"zsh",
-		"bash",
-		"lua",
-		"luau",
-	},
-}
-lsp.format_on_save({
-	format_opts = {
-		async = true,
-	},
-	servers = format_servers,
-})
-lsp.format_mapping("gq", {
-	format_opts = {
-		async = false,
-	},
-	servers = format_servers,
-})
-
-lsp.setup()
-
-local null_ls = require("null-ls")
-null_ls.setup({})
-require("mason-null-ls").setup({
-	ensure_installed = { "black", "prettier", "shfmt", "eslint-lsp", "stylua", "jq" },
-	automatic_installation = false,
-	handlers = {
-		shfmt = function(_, _)
-			null_ls.register(null_ls.builtins.formatting.shfmt.with({
-				extra_filetypes = { "bash", "zsh" },
-			}))
-		end,
-		prettier = function(_, _)
-			null_ls.register(null_ls.builtins.formatting.prettier.with({
-				extra_filetypes = { "astro" },
-			}))
-		end,
-		eslint = function(_, _)
-			null_ls.register(null_ls.builtins.diagnostics.eslint.with({
-				extra_filetypes = { "astro" },
-			}))
-			null_ls.register(null_ls.builtins.code_actions.eslint.with({
-				extra_filetypes = { "astro" },
-			}))
-		end,
-	},
-})
-
-local luasnip = require("luasnip")
-local has_words_before = function()
-	local line, col = unpack(vim.api.nvim_win_get_cursor(0))
-	return col ~= 0 and vim.api.nvim_buf_get_lines(0, line - 1, line, true)[1]:sub(col, col):match("%s") == nil
-end
-
-local kind_icons = {
-	Text = "",
-	Method = "",
-	Function = "",
-	Constructor = "",
-	Field = "",
-	Variable = "",
-	Class = "ﴯ",
-	Interface = "",
-	Module = "",
-	Property = "ﰠ",
-	Unit = "",
-	Value = "",
-	Enum = "",
-	Keyword = "",
-	Snippet = "",
-	Color = "",
-	File = "",
-	Reference = "",
-	Folder = "",
-	EnumMember = "",
-	Constant = "",
-	Struct = "",
-	Event = "",
-	Operator = "",
-	TypeParameter = "",
-}
-local cmp = require("cmp")
-cmp.setup({
-	window = { documentation = cmp.config.window.bordered() },
-	snippet = {
-		expand = function(args)
-			require("luasnip").lsp_expand(args.body)
-		end,
-	},
-	sources = {
-		{ name = "nvim_lsp" },
-		{ name = "otter" },
-		{ name = "luasnip", keyword_length = 2 },
-		{ name = "pandoc_references" },
-		{ name = "nvim_lua" },
-		{
-			name = "beancount",
-			option = {
-				account = vim.env["HOME"] .. "/documents/records/budget/main.beancount", -- TODO implement dynamically
-			},
-		},
-		{ name = "calc" },
-		{ name = "path" },
-		{ name = "buffer", keyword_length = 3 },
-		{ name = "digraphs" },
-		{ name = "latex_symbols" },
-		{ name = "spell", keyword_length = 3 },
-		{ name = "tmux" }, -- { name = 'rg',           keyword_length = 5 },
-		{ name = "vCard" },
-	},
-	mapping = cmp.mapping.preset.insert({
-		["<C-b>"] = cmp.mapping.scroll_docs(-4),
-		["<C-f>"] = cmp.mapping.scroll_docs(4),
-		["<CR>"] = cmp.mapping({
-			i = function(fallback)
-				if cmp.visible() and cmp.get_active_entry() then
-					cmp.confirm({
-						behavior = cmp.ConfirmBehavior.Replace,
-						select = false,
-					})
-				else
-					fallback()
-				end
-			end,
-			s = cmp.mapping.confirm({ select = true }),
-			c = cmp.mapping.confirm({
-				behavior = cmp.ConfirmBehavior.Replace,
-				select = false,
-			}), -- disable selection in cmd mode
-		}),
-		["<Tab>"] = cmp.mapping(function(fallback)
-			if cmp.visible() then
-				cmp.select_next_item()
-				-- You could replace the expand_or_jumpable() calls with expand_or_locally_jumpable()
-				-- they way you will only jump inside the snippet region
-			elseif luasnip.expand_or_jumpable() then
-				luasnip.expand_or_jump()
-			elseif has_words_before() then
-				cmp.complete()
-			else
-				fallback()
-			end
-		end, { "i", "s" }),
-		["<S-Tab>"] = cmp.mapping(function(fallback)
-			if cmp.visible() then
-				cmp.select_prev_item()
-			elseif luasnip.jumpable(-1) then
-				luasnip.jump(-1)
-			else
-				fallback()
-			end
-		end, { "i", "s" }),
-	}),
-	formatting = {
-		fields = { "kind", "abbr", "menu" },
-		format = function(entry, vim_item)
-			-- Kind icons, removing kind text leaving only icon
-			-- vim_item.kind = string.format('%s %s', kind_icons[vim_item.kind], vim_item.kind)
-			vim_item.kind = string.format("%s", kind_icons[vim_item.kind])
-			-- Source
-			vim_item.menu = ({
-				buffer = "[Buf]",
-				calc = "[Cal]",
-				digraphs = "[Dig]",
-				latex_symbols = "[LaTeX]",
-				luasnip = "[Snip]",
-				nvim_lsp = "[Lsp]",
-				nvim_lua = "[Lua]",
-				pandoc_references = "[Bib]",
-				spell = "[Spl]",
-				vCard = "[vCrd]",
-			})[entry.source.name]
-			return vim_item
-		end,
-	},
-})
--- `/` cmdline setup.
-cmp.setup.cmdline("/", {
-	mapping = cmp.mapping.preset.cmdline(),
-	sources = { { name = "buffer" } },
-})
--- `:` cmdline setup.
-cmp.setup.cmdline(":", {
-	mapping = cmp.mapping.preset.cmdline(),
-	sources = cmp.config.sources({ { name = "path" } }, {
-		{ name = "cmdline", option = { ignore_cmds = { "Man", "!" } } },
-	}),
-})

nvim/.config/nvim/lua/plug/_telescope.lua

@@ -1,64 +0,0 @@
--- Setup up telescope fuzzy finding settings
---
--- Makes use of optionally installed external programs to work fully:
--- rg (ripgrep) for in-text searches
--- fd for quicker directory structure searches
--- lsp for a variety of lsp queries
-require("telescope").setup({
-	defaults = {
-		vimgrep_arguments = {
-			"rg",
-			"--ignore-vcs",
-			"--hidden",
-			"--color=never",
-			"--no-heading",
-			"--with-filename",
-			"--line-number",
-			"--column",
-			"--smart-case",
-		},
-		generic_sorter = require("mini.fuzzy").get_telescope_sorter,
-	},
-	defaults = {
-		-- Appearance
-		prompt_prefix = "  ",
-		selection_caret = "󰳟 ",
-		color_devicons = true,
-	},
-	pickers = {
-		buffers = { theme = "ivy" },
-		oldfiles = { theme = "ivy" },
-		find_files = {
-			theme = "dropdown",
-			-- nice minimal picker design
-			borderchars = {
-				{ "─", "│", "─", "│", "┌", "┐", "┘", "└" },
-				prompt = { "─", "│", " ", "│", "┌", "┐", "│", "│" },
-				results = {
-					"─",
-					"│",
-					"─",
-					"│",
-					"├",
-					"┤",
-					"┘",
-					"└",
-				},
-				preview = {
-					"─",
-					"│",
-					"─",
-					"│",
-					"┌",
-					"┐",
-					"┘",
-					"└",
-				},
-			},
-			width = 0.8,
-			previewer = false,
-			prompt_title = false,
-		},
-	},
-})
-require("telescope").load_extension("fzf")

nvim/.config/nvim/lua/plug/_toggleterm.lua

@@ -1,18 +0,0 @@
-require("toggleterm").setup({
-	open_mapping = [[<leader>=]],
-	insert_mappings = false, -- don't map the key in insert mode
-})
-
-local Terminal = require("toggleterm.terminal").Terminal
--- create a lazygit window with the lazygit command
-local lazygit = Terminal:new({
-	cmd = "lazygit",
-	hidden = true,
-	direction = "float",
-	float_opts = { border = "curved" },
-})
-function _Lazygit_toggle()
-	lazygit:toggle()
-end
-
-vim.cmd([[command! Lazygit :lua _Lazygit_toggle()<cr>]])

nvim/.config/nvim/lua/plug/_treesitter.lua

@@ -1,21 +0,0 @@
-local rainbow = require("ts-rainbow")
-require("nvim-treesitter.configs").setup({
-	-- one of "all", "maintained" (parsers with maintainers), or a list of languages
-	ensure_installed = "all",
-	highlight = { enable = true },
-	incremental_selection = { enable = true },
-	textobjects = { enable = true },
-	indent = { enable = true },
-
-	-- enable rainbow brackets, needs p00f/nvim-ts-rainbow
-	rainbow = {
-		enable = true,
-		strategy = { rainbow.strategy.global },
-	},
-
-	-- for improved commentstrings, needs corresponding plugin
-	context_commentstring = {
-		enable = true,
-		enable_autocmd = false, -- since we run it as a hook from the mini.comment plugin
-	},
-})

nvim/.config/nvim/lua/plugins.lua

@@ -1,321 +0,0 @@
-local writing_ft = { "quarto", "pandoc", "markdown", "text", "tex" }
-
-return {
-	-- essential
-	{ "numToStr/Navigator.nvim", branch = "master", config = true }, -- allow seamless navigation between vim buffers and tmux/wezterm splits
-	{ "jeffkreeftmeijer/vim-numbertoggle", event = "BufEnter" }, -- toggles numbers to absolute for all buffers but the current which is relative
-	{ "ojroques/vim-oscyank", event = "VeryLazy" }, -- yank from *anywhere* (even ssh session) to clipboard, using :OSCYank
-	{ "ggandor/lightspeed.nvim", event = "VeryLazy" }, -- jump between letters with improved fFtT quicksearch, mimics sneak
-	{
-		"lewis6991/gitsigns.nvim", -- show vcs changes on left-hand gutter
-		config = function()
-			require("plug._gitsigns")
-		end,
-		event = "BufRead",
-	},
-	{ "m4xshen/smartcolumn.nvim", config = true }, -- auto-hiding colorcolumn
-	-- files
-	{ "vifm/vifm.vim" }, -- integrate file manager
-	{
-		"nvim-tree/nvim-tree.lua", -- integrate file tree
-		config = true,
-		dependencies = { "nvim-tree/nvim-web-devicons", config = true },
-		cmd = "NvimTreeToggle",
-	}, -- colors
-	{
-		"RRethy/nvim-base16",
-		event = "BufWinEnter",
-		dependencies = { "rktjmp/fwatch.nvim" },
-	},
-	{
-		"NvChad/nvim-colorizer.lua", -- color hex, named colors in the correct preview scheme
-		config = function()
-			require("colorizer").setup({
-				user_default_options = { mode = "virtualtext" },
-			})
-		end,
-		event = "VeryLazy",
-	}, -- editing
-	{ "kylechui/nvim-surround", version = "*", config = true, event = "VeryLazy" }, -- surround things with other things using ys/cs/ds
-	{
-		"monaqa/dial.nvim", -- extend the ^a / ^x possibilities to dates, hex, alphabets, markdown headers
-		config = function()
-			local augend = require("dial.augend")
-			require("dial.config").augends:register_group({
-				-- default augends used when no group name is specified
-				default = {
-					augend.integer.alias.decimal,
-					augend.integer.alias.hex,
-					augend.date.alias["%Y/%m/%d"],
-					augend.date.alias["%Y-%m-%d"],
-					augend.date.alias["%m/%d"],
-					augend.date.alias["%H:%M:%S"],
-					augend.date.alias["%H:%M"],
-					augend.constant.alias.de_weekday_full,
-					augend.constant.alias.de_weekday,
-					augend.constant.alias.bool,
-					augend.semver.alias.semver,
-					augend.constant.alias.Alpha,
-					augend.constant.alias.alpha,
-					augend.hexcolor.new({ case = "lower" }),
-					augend.constant.new({
-						elements = { "and", "or" },
-						word = true, -- if false, "sand" is incremented into "sor", "doctor" into "doctand", etc.
-						cyclic = true, -- "or" is incremented into "and".
-					}),
-					augend.constant.new({
-						elements = { "&&", "||" },
-						word = false,
-						cyclic = true,
-					}),
-				},
-			})
-		end,
-		event = "VeryLazy",
-	},
-	{
-		"tommcdo/vim-exchange", -- adds exchange operator with cx. common use: cxiw . on 2 words to switch
-		event = "VeryLazy",
-	},
-	{
-		"junegunn/vim-easy-align", -- Align tables and other alignable things
-		event = "VeryLazy",
-	},
-	{ "edKotinsky/Arduino.nvim", ft = "arduino", config = true }, -- statusline
-	{
-		"nvim-lualine/lualine.nvim",
-		requires = { "nvim-tree/nvim-web-devicons", config = true },
-		config = function()
-			require("plug._lualine")
-		end,
-	}, -- writing
-	{ "vim-pandoc/vim-criticmarkup", ft = writing_ft },
-	{
-		"jbyuki/nabla.nvim",
-		ft = writing_ft,
-		config = function()
-			require("nabla").enable_virt({ autogen = true, silent = true })
-		end,
-	},
-	{
-		"mickael-menu/zk-nvim",
-		config = function()
-			require("zk").setup({ picker = "telescope" })
-		end,
-	},
-	{
-		"andrewferrier/wrapping.nvim",
-		config = function()
-			require("wrapping").setup({
-				create_keymappings = false,
-				notify_on_switch = false,
-			})
-		end,
-	},
-	{
-		"quarto-dev/quarto-nvim",
-		dependencies = {
-			"jmbuhr/otter.nvim",
-			"neovim/nvim-lspconfig",
-			"vim-pandoc/vim-pandoc-syntax",
-			"hrsh7th/nvim-cmp",
-			"nvim-treesitter/nvim-treesitter",
-		},
-		config = function()
-			require("quarto").setup({
-				lspFeatures = {
-					enabled = true,
-					languages = { "r", "python", "julia" },
-					diagnostics = { enabled = true, triggers = { "BufWrite" } },
-					completion = { enabled = true },
-				},
-			})
-		end,
-		ft = "quarto",
-	},
-	{
-		"lkhphuc/jupyter-kernel.nvim",
-		config = true,
-		cmd = "JupyterAttach",
-		build = ":UpdateRemotePlugins",
-		keys = {
-			{
-				"<localleader>ck",
-				"<Cmd>JupyterInspect<CR>",
-				desc = "Inspect object in kernel",
-			},
-		},
-	},
-	{ "micarmst/vim-spellsync", event = "VeryLazy" }, -- personal dict improvements for git sync
-	{ "folke/zen-mode.nvim", config = true, event = "VeryLazy" }, -- provide distraction free writing
-	{ "folke/twilight.nvim", event = "VeryLazy" }, -- provide even distraction free-er writing (lowlight paragraphs)
-	{
-		"JellyApple102/easyread.nvim",
-		config = true,
-		ft = writing_ft,
-		cmd = "EasyreadToggle",
-	}, -- enable 'speed-reading' mode (bionic reading)
-	{ "marty-oehme/zettelkasten.nvim", ft = writing_ft, event = "VeryLazy" }, -- simple static markdown linking
-	{
-		"iamcco/markdown-preview.nvim", -- generate an auto-updating html preview for md files
-		build = function()
-			vim.fn["mkdp#util#install"]()
-		end,
-		ft = writing_ft,
-	}, -- languages
-	{ "euclidianAce/BetterLua.vim", ft = "lua" }, -- better syntax highlighting for lua
-	{ "aliou/bats.vim", ft = { "bash", "sh", "zsh", "bats" } }, -- enable syntax for bats shell-code testing library
-
-	-- REPL work
-	{
-		"WhiteBlackGoose/magma-nvim-goose",
-		build = ":UpdateRemotePlugins",
-		config = function()
-			vim.g.magma_image_provider = "kitty"
-			vim.g.magma_automatically_open_output = false
-		end,
-	},
-	{
-		"echasnovski/mini.nvim",
-		version = "*",
-		config = function()
-			require("plug._mini")
-		end,
-	},
-	{
-		"akinsho/nvim-toggleterm.lua", -- simpler, programmable and multiple terminal toggling for nvim
-		config = function()
-			require("plug._toggleterm")
-		end,
-	},
-	{
-		"folke/which-key.nvim",
-		config = function()
-			require("which-key").setup({})
-		end,
-	}, -- fuzzy matching
-	{ "nvim-telescope/telescope-fzf-native.nvim", build = "make" },
-	{
-		"nvim-telescope/telescope.nvim",
-		dependencies = { "nvim-lua/popup.nvim", "nvim-lua/plenary.nvim" },
-		config = function()
-			require("plug._telescope")
-		end,
-	},
-	{
-		"dense-analysis/neural",
-		dependencies = { "MunifTanjim/nui.nvim", "elpiloto/significant.nvim" },
-		config = function()
-			require("neural").setup({
-				source = { openai = { api_key = vim.env.OPENAI_API_KEY } },
-			})
-		end,
-	}, -- treesitter
-	{
-		"nvim-treesitter/nvim-treesitter",
-		build = ":TSUpdate",
-		config = function()
-			require("plug._treesitter")
-		end,
-		event = "BufReadPre",
-		-- rainbow brackets using treesitter
-		-- show current cursor context at top of buffer
-		-- improves commenting plugin above by using ts
-		dependencies = {
-			"https://gitlab.com/HiPhish/nvim-ts-rainbow2.git",
-			{ "romgrk/nvim-treesitter-context", config = true },
-			"JoosepAlviste/nvim-ts-context-commentstring",
-		},
-	},
-	{ "nvim-treesitter/playground", cmd = "TSPlaygroundToggle" }, -- interactively view and query the treesitter tree
-	{
-		"RRethy/nvim-treesitter-textsubjects", -- allows using . and ; to target treesitter branches
-		config = function()
-			require("nvim-treesitter.configs").setup({
-				textsubjects = {
-					enable = true,
-					keymaps = {
-						["."] = "textsubjects-smart",
-						[";"] = "textsubjects-container-outer",
-					},
-				},
-			})
-		end,
-		event = "BufReadPre",
-	},
-	{
-		-- lsp
-		"VonHeikemen/lsp-zero.nvim",
-		dependencies = {
-			{ "neovim/nvim-lspconfig", branch = "master" },
-			"williamboman/mason.nvim",
-			"williamboman/mason-lspconfig.nvim",
-			{
-				"hrsh7th/nvim-cmp",
-				branch = "main",
-				dependencies = {
-					"andersevenrud/cmp-tmux",
-					"cbarrete/completion-vcard",
-					"f3fora/cmp-spell",
-					"hrsh7th/cmp-nvim-lsp",
-					"hrsh7th/cmp-path",
-					"hrsh7th/cmp-buffer",
-					"hrsh7th/cmp-calc",
-					"hrsh7th/cmp-cmdline",
-					"hrsh7th/cmp-nvim-lua",
-					"dmitmel/cmp-digraphs",
-					"jc-doyle/cmp-pandoc-references",
-					"kdheepak/cmp-latex-symbols",
-					"lukas-reineke/cmp-rg",
-					"crispgm/cmp-beancount",
-					"ray-x/cmp-treesitter",
-					"saadparwaiz1/cmp_luasnip",
-				},
-			},
-			"L3MON4D3/LuaSnip",
-			"rafamadriz/friendly-snippets",
-			-- { "lukas-reineke/lsp-format.nvim", config = true },
-			{ "j-hui/fidget.nvim", config = true }, -- loading animations for some LSP
-			{
-				"jay-babu/mason-null-ls.nvim",
-				event = { "BufReadPre", "BufNewFile" },
-				dependencies = {
-					"williamboman/mason.nvim",
-					"jose-elias-alvarez/null-ls.nvim",
-				},
-			},
-		},
-		config = function()
-			require("plug._lsp")
-		end,
-		branch = "v2.x",
-	},
-	{ "simrat39/symbols-outline.nvim", config = true, event = "VeryLazy" }, -- vista-like outline view for code
-	{ "ray-x/lsp_signature.nvim", config = true }, -- UI improvements
-	{ "stevearc/dressing.nvim", config = true },
-	{
-		"rcarriga/nvim-notify",
-		config = function()
-			vim.notify = require("notify")
-		end,
-	},
-	-- { -- REQUIRES custom `yay -S --asdeps lua51-lyaml invocation` AND is suuper slow
-	--     "jghauser/papis.nvim",
-	--     after = { "telescope.nvim", "nvim-cmp" },
-	--     dependencies = {
-	--         "kkharji/sqlite.lua", "nvim-lua/plenary.nvim",
-	--         "MunifTanjim/nui.nvim", "nvim-treesitter/nvim-treesitter"
-	--     },
-	--     ft = writing_ft,
-	--     rocks = { "lyaml" },
-	--     config = function()
-	--         require('papis').setup({
-	--             papis_python = {
-	--                 dir = "/home/marty/documents/library/academia",
-	--                 info_name = "info.yaml",
-	--                 notes_name = [[notes.qmd]]
-	--             }
-	--         })
-	--     end
-	-- }
-}

nvim/.config/nvim/lua/plugins/config/cmp.lua

@@ -0,0 +1,142 @@
+local luasnip = require("luasnip")
+local cmp = require("cmp")
+
+local has_words_before = function()
+	local line, col = unpack(vim.api.nvim_win_get_cursor(0))
+	return col ~= 0 and vim.api.nvim_buf_get_lines(0, line - 1, line, true)[1]:sub(col, col):match("%s") == nil
+end
+
+local kind_icons = {
+	Text = "",
+	Method = "",
+	Function = "",
+	Constructor = "",
+	Field = "",
+	Variable = "",
+	Class = "ﴯ",
+	Interface = "",
+	Module = "",
+	Property = "ﰠ",
+	Unit = "",
+	Value = "",
+	Enum = "",
+	Keyword = "",
+	Snippet = "",
+	Color = "",
+	File = "",
+	Reference = "",
+	Folder = "",
+	EnumMember = "",
+	Constant = "",
+	Struct = "",
+	Event = "",
+	Operator = "",
+	TypeParameter = "",
+}
+
+cmp.setup({
+	window = { documentation = cmp.config.window.bordered() },
+	snippet = {
+		expand = function(args)
+			require("luasnip").lsp_expand(args.body)
+		end,
+	},
+	sources = {
+		{ name = "nvim_lsp" },
+		{ name = "otter" },
+		{ name = "luasnip", keyword_length = 2 },
+		{ name = "pandoc_references" },
+		{ name = "nvim_lua" },
+		{
+			name = "beancount",
+			option = {
+				account = vim.env["HOME"] .. "/documents/records/budget/main.beancount", -- TODO implement dynamically
+			},
+		},
+		{ name = "calc" },
+		{ name = "path" },
+		{ name = "buffer", keyword_length = 3 },
+		{ name = "digraphs" },
+		{ name = "latex_symbols" },
+		{ name = "spell", keyword_length = 3 },
+		{ name = "tmux" }, -- { name = 'rg',           keyword_length = 5 },
+		{ name = "vCard" },
+	},
+	mapping = cmp.mapping.preset.insert({
+		["<C-b>"] = cmp.mapping.scroll_docs(-4),
+		["<C-f>"] = cmp.mapping.scroll_docs(4),
+		["<CR>"] = cmp.mapping({
+			i = function(fallback)
+				if cmp.visible() and cmp.get_active_entry() then
+					cmp.confirm({
+						behavior = cmp.ConfirmBehavior.Replace,
+						select = false,
+					})
+				else
+					fallback()
+				end
+			end,
+			s = cmp.mapping.confirm({ select = true }),
+			c = cmp.mapping.confirm({
+				behavior = cmp.ConfirmBehavior.Replace,
+				select = false,
+			}), -- disable selection in cmd mode
+		}),
+		["<Tab>"] = cmp.mapping(function(fallback)
+			if cmp.visible() then
+				cmp.select_next_item()
+				-- You could replace the expand_or_jumpable() calls with expand_or_locally_jumpable()
+				-- they way you will only jump inside the snippet region
+			elseif luasnip.expand_or_jumpable() then
+				luasnip.expand_or_jump()
+			elseif has_words_before() then
+				cmp.complete()
+			else
+				fallback()
+			end
+		end, { "i", "s" }),
+		["<S-Tab>"] = cmp.mapping(function(fallback)
+			if cmp.visible() then
+				cmp.select_prev_item()
+			elseif luasnip.jumpable(-1) then
+				luasnip.jump(-1)
+			else
+				fallback()
+			end
+		end, { "i", "s" }),
+	}),
+	formatting = {
+		fields = { "kind", "abbr", "menu" },
+		format = function(entry, vim_item)
+			-- Kind icons, removing kind text leaving only icon
+			-- vim_item.kind = string.format('%s %s', kind_icons[vim_item.kind], vim_item.kind)
+			vim_item.kind = string.format("%s", kind_icons[vim_item.kind])
+			-- Source
+			vim_item.menu = ({
+				buffer = "[Buf]",
+				calc = "[Cal]",
+				digraphs = "[Dig]",
+				latex_symbols = "[LaTeX]",
+				luasnip = "[Snip]",
+				nvim_lsp = "[Lsp]",
+				nvim_lua = "[Lua]",
+				pandoc_references = "[Bib]",
+				spell = "[Spl]",
+				vCard = "[vCrd]",
+			})[entry.source.name]
+			return vim_item
+		end,
+	},
+})
+-- `/` cmdline setup.
+cmp.setup.cmdline("/", {
+	mapping = cmp.mapping.preset.cmdline(),
+	sources = { { name = "buffer" } },
+})
+-- `:` cmdline setup.
+cmp.setup.cmdline(":", {
+	mapping = cmp.mapping.preset.cmdline(),
+	sources = cmp.config.sources({ { name = "path" } }, {
+		{ name = "cmdline", option = { ignore_cmds = { "Man", "!" } } },
+	}),
+})

nvim/.config/nvim/lua/plugins/config/lsp.lua

@@ -0,0 +1,168 @@
+vim.diagnostic.config({ virtual_text = true })
+vim.fn.sign_define("DiagnosticSignError", { text = "✘", texthl = "DiagnosticSignError" })
+vim.fn.sign_define("DiagnosticSignWarn", { text = "", texthl = "DiagnosticSignWarn" })
+vim.fn.sign_define("DiagnosticSignInfo", { text = "", texthl = "DiagnosticSignInfo" })
+vim.fn.sign_define("DiagnosticSignHint", { text = "", texthl = "DiagnosticSignHint" })
+
+local lsp = require("lsp-setup")
+
+local servers = {
+	ansiblels = {},
+	arduino_language_server = {},
+	astro = {},
+	bashls = {},
+	beancount = {},
+	clangd = {},
+	cssls = {},
+	docker_compose_language_service = {},
+	dockerls = {},
+	emmet_ls = {},
+	gopls = {},
+	julials = {},
+	lua_ls = {
+		settings = {
+			Lua = {
+				diagnostics = { globals = { "vim" } },
+				-- enable when working on neovim stuff. Takes *long* to load
+				-- workspace = { library = vim.api.nvim_get_runtime_file("", true) },
+				telemetry = { enable = false },
+			},
+		},
+	},
+	marksman = {},
+	pyright = {},
+	ruff_lsp = {},
+	tailwindcss = {},
+	taplo = {},
+	texlab = {},
+	tsserver = {},
+	yamlls = {},
+	zk = {},
+}
+
+local function on_attach(client, bufnr)
+	local map = vim.keymap.set
+	map("n", "[d", "<cmd>lua vim.diagnostic.goto_prev()<cr>", { buffer = bufnr, desc = "Previous diagnostic" })
+	map("n", "]d", "<cmd>lua vim.diagnostic.goto_next()<cr>", { buffer = bufnr, desc = "Next diagnostic" })
+	map(
+		"n",
+		"[e",
+		"<cmd>lua vim.diagnostic.goto_prev({severity = vim.diagnostic.severity.ERROR})<cr>",
+		{ buffer = bufnr, desc = "Previous error" }
+	)
+	map(
+		"n",
+		"]e",
+		"<cmd>lua vim.diagnostic.goto_next({severity = vim.diagnostic.severity.ERROR})<cr>",
+		{ buffer = bufnr, desc = "Next error" }
+	)
+
+	local prefix = require("which-key").register
+	prefix({ ["<localleader>l"] = { name = "+lsp" } })
+	map("n", "<localleader>li", "<cmd>LspInfo<cr>", { buffer = bufnr, desc = "Lsp Info" })
+	map(
+		"n",
+		"<localleader>ld",
+		"<cmd>lua vim.diagnostic.open_float()<cr>",
+		{ buffer = bufnr, desc = "Line diagnostics" }
+	)
+	map("n", "<localleader>la", "<cmd>lua vim.lsp.buf.code_action()<cr>", { buffer = bufnr, desc = "Codeactions" })
+	map("n", "<localleader>ln", "<cmd>lua vim.lsp.buf.rename()<cr>", { buffer = bufnr, desc = "Rename element" })
+	if vim.fn.exists(":Telescope") then
+		map("n", "<localleader>lr", "<cmd>Telescope lsp_references<cr>", { buffer = bufnr, desc = "References" })
+		map("n", "<localleader>lf", "<cmd>Telescope lsp_definitions<cr>", { buffer = bufnr, desc = "Definition" })
+		map(
+			"n",
+			"<localleader>lt",
+			"<cmd>Telescope lsp_type_definitions<cr>",
+			{ buffer = bufnr, desc = "Type definition" }
+		)
+		map(
+			"n",
+			"<localleader>lm",
+			"<cmd>Telescope lsp_implementations<cr>",
+			{ buffer = bufnr, desc = "Implementation" }
+		)
+	else
+		map("n", "<localleader>lr", "<cmd>lua vim.lsp.buf.references()<cr>", { buffer = bufnr, desc = "References" })
+		map("n", "<localleader>lf", "<cmd>lua vim.lsp.buf.definition()<cr>", { buffer = bufnr, desc = "Definition" })
+		map(
+			"n",
+			"<localleader>lt",
+			"<cmd>lua vim.lsp.buf.type_definition()<cr>",
+			{ buffer = bufnr, desc = "Type definition" }
+		)
+		map(
+			"n",
+			"<localleader>lm",
+			"<cmd>lua vim.lsp.buf.implementation()<cr>",
+			{ buffer = bufnr, desc = "Implementation" }
+		)
+	end
+	map("n", "<localleader>ll", "<cmd>lua vim.lsp.buf.format()<CR>", { buffer = bufnr, desc = "Format document" })
+	map("n", "K", "<cmd>lua vim.lsp.buf.hover()<cr>", { buffer = bufnr, desc = "Hover definition" })
+	map("n", "<localleader>lc", "<cmd>lua vim.lsp.buf.declaration()<cr>", { buffer = bufnr, desc = "Declaration" })
+	map(
+		"n",
+		"<localleader>ls",
+		"<cmd>lua vim.lsp.buf.signature_help()<cr>",
+		{ buffer = bufnr, desc = "Signature help" }
+	)
+
+	if vim.g.format_on_save then
+		require("lsp-setup.utils").format_on_save(client)
+    end
+end
+
+lsp.setup({
+	default_mappings = false,
+	servers = servers,
+	on_attach = on_attach,
+	inlay_hints = {
+		enabled = vim.fn.has("nvim-0.10") == true and true or false,
+	},
+})
+
+local lspconfig = require("lspconfig")
+
+-- ensure python virtualenv is determined automatically on lsp start
+lspconfig.pyright.setup({
+	on_attach = function(client, _)
+		local python_path, msg = require("util.pyenv").get_path(client.config.root_dir)
+		vim.notify(string.format("%s\n%s", msg, python_path))
+		client.config.settings.python.pythonPath = python_path
+	end,
+})
+-- set up arduino with the help of arduino.nvim plugin
+if require("util").is_available("arduino") then
+	lspconfig.arduino_language_server.setup({
+		on_new_config = require("arduino").on_new_config,
+	})
+end
+
+local null_ls = require("null-ls")
+null_ls.setup({})
+require("mason-null-ls").setup({
+	ensure_installed = { "black", "prettier", "shfmt", "eslint-lsp", "stylua", "jq" },
+	automatic_installation = false,
+	handlers = {
+		shfmt = function(_, _)
+			null_ls.register(null_ls.builtins.formatting.shfmt.with({
+				extra_filetypes = { "bash", "zsh" },
+			}))
+		end,
+		prettier = function(_, _)
+			null_ls.register(null_ls.builtins.formatting.prettier.with({
+				extra_filetypes = { "astro" },
+			}))
+		end,
+		eslint = function(_, _)
+			null_ls.register(null_ls.builtins.diagnostics.eslint.with({
+				extra_filetypes = { "astro" },
+			}))
+			null_ls.register(null_ls.builtins.code_actions.eslint.with({
+				extra_filetypes = { "astro" },
+			}))
+		end,
+	},
+})

nvim/.config/nvim/lua/plugins/config/mini.lua

@@ -14,7 +14,7 @@ require("mini.indentscope").setup({
 	options = { indent_at_cursor = false },
 })
 require("mini.map").setup()
--- require('mini.move').setup() -- has not hit stable yet
+require("mini.move").setup() -- has not hit stable yet
 require("mini.pairs").setup()
 require("mini.trailspace").setup()
 

nvim/.config/nvim/lua/plugins/config/toggleterm.lua

@@ -0,0 +1,85 @@
+require("toggleterm").setup({
+	open_mapping = [[<leader>=]],
+	insert_mappings = false, -- don't map the key in insert mode
+	terminal_mappings = false,
+})
+
+local Terminal = require("toggleterm.terminal").Terminal
+
+-- need to disable indentlines since they obscure first line of terminal
+if require("util").is_available("mini.nvim") then
+	vim.api.nvim_create_autocmd({ "TermOpen" }, {
+		pattern = "*",
+		callback = function()
+			vim.b.miniindentscope_disable = true
+		end,
+	})
+end
+
+local function custom_term_set_toggle_key(term)
+	vim.keymap.set("t", "<C-\\>", function()
+		term:toggle()
+	end, { silent = true, buffer = true })
+end
+
+-- create python window
+local function get_python_cmd()
+	if vim.fn.executable("ptipython") then
+		return "ptipython"
+	end
+	if vim.fn.executable("ipython") then
+		return "ipython"
+	end
+	if vim.fn.executable("ptpython") then
+		return "ptpython"
+	end
+	if vim.fn.executable("python") then
+		return "python"
+	end
+end
+local terms = {
+	lazygit = Terminal:new({
+		cmd = "lazygit",
+		hidden = true,
+		direction = "float",
+		float_opts = { border = "curved" },
+		on_open = custom_term_set_toggle_key,
+	}),
+	python = Terminal:new({
+		cmd = get_python_cmd(),
+		hidden = true,
+		direction = "float",
+		float_opts = { border = "curved" },
+		on_open = custom_term_set_toggle_key,
+	}),
+}
+-- create a lazygit window with the lazygit command
+local function toggle_custom_term(term, bang, vertsize)
+	vertsize = vertsize or vim.o.columns * 0.4
+	if not bang then
+		term.direction = "float"
+		term:toggle()
+	else
+		term.direction = "vertical"
+		term:resize(vertsize)
+		term:toggle()
+	end
+end
+
+local function _Pythonterm_toggle(opts)
+	toggle_custom_term(terms.python, opts.bang)
+end
+local function _Lazygit_toggle(opts)
+	toggle_custom_term(terms.lazygit, opts.bang, vim.o.columns * 0.6)
+end
+
+vim.api.nvim_create_user_command(
+    "Lazygit",
+    _Lazygit_toggle,
+    { desc = "Toggle floating Lazygit terminal", bang = true }
+)
+vim.api.nvim_create_user_command(
+	"Pythonterm",
+	_Pythonterm_toggle,
+	{ desc = "Toggle floating Python terminal", bang = true }
+)

nvim/.config/nvim/lua/plugins/core.lua

@@ -0,0 +1,46 @@
+return {
+	-- allow seamless navigation between vim buffers and tmux/wezterm splits
+	{
+		"numToStr/Navigator.nvim",
+		branch = "master",
+		config = true,
+		event = "VeryLazy",
+	},
+	-- jump between letters with improved fFtT quicksearch, mimics sneak
+	{ "ggandor/lightspeed.nvim", event = "VeryLazy" },
+
+	-- yank from *anywhere* (even ssh session) to clipboard, using :OSCYank
+	{ "ojroques/vim-oscyank", event = "VeryLazy" },
+	-- personal dict improvements for git sync
+	{ "micarmst/vim-spellsync", event = "VeryLazy" },
+	{
+		"folke/which-key.nvim",
+		config = true,
+		event = "VeryLazy",
+	},
+	-- collection of plugins
+	{
+		"echasnovski/mini.nvim",
+		version = "*",
+		config = function()
+			require("plugins.config.mini")
+		end,
+		event = "VimEnter", -- need to load pretty soon for Starter screen
+	},
+	-- simpler, programmable and multiple terminal toggling for nvim
+	{
+		"akinsho/nvim-toggleterm.lua",
+		config = function()
+			require("plugins.config.toggleterm")
+		end,
+		lazy = false,
+		cmd = { "ToggleTerm", "TermExec", "Lazygit", "Pythonterm" },
+	},
+	-- colorschemes
+	{
+		"RRethy/nvim-base16",
+		lazy = false,
+		priority = 1000,
+		dependencies = { "rktjmp/fwatch.nvim" },
+	},
+}

nvim/.config/nvim/lua/plugins/data_analysis.lua

@@ -0,0 +1,55 @@
+return {
+	{
+		"quarto-dev/quarto-nvim",
+		dependencies = {
+			"jmbuhr/otter.nvim",
+			"neovim/nvim-lspconfig",
+			"vim-pandoc/vim-pandoc-syntax",
+			"hrsh7th/nvim-cmp",
+			"nvim-treesitter/nvim-treesitter",
+		},
+		config = function()
+			require("quarto").setup({
+				lspFeatures = {
+					enabled = true,
+					languages = { "r", "python", "julia" },
+					diagnostics = { enabled = true, triggers = { "BufWrite" } },
+					completion = { enabled = true },
+				},
+			})
+		end,
+		ft = "quarto",
+	},
+
+	{
+		"lkhphuc/jupyter-kernel.nvim",
+		config = true,
+		cmd = "JupyterAttach",
+		build = ":UpdateRemotePlugins",
+		keys = {
+			{
+				"<localleader>ck",
+				"<Cmd>JupyterInspect<CR>",
+				desc = "Inspect object in kernel",
+			},
+		},
+	},
+
+	-- REPL work
+	{
+		"WhiteBlackGoose/magma-nvim-goose",
+		build = ":UpdateRemotePlugins",
+		config = function()
+			vim.g.magma_image_provider = "kitty"
+			vim.g.magma_automatically_open_output = false
+		end,
+		cmd = {
+			"MagmaInit",
+			"MagmaEvaluateOperator",
+			"MagmaEvaluateLine",
+			"MagmaEvaluateVisual",
+			"MagmaRestart",
+		},
+		ft = { "quarto", "python" },
+	},
+}

nvim/.config/nvim/lua/plugins/editing.lua

@@ -0,0 +1,52 @@
+return {
+	-- adds exchange operator with cx. common use: cxiw . on 2 words to switch
+	{
+		"tommcdo/vim-exchange",
+		event = "VeryLazy",
+	},
+	-- Align tables and other alignable things
+	{
+		"junegunn/vim-easy-align",
+		event = "VeryLazy",
+	},
+	-- surround things with other things using ys/cs/ds
+	{ "kylechui/nvim-surround", version = "*", config = true, event = "VeryLazy" },
+
+	-- extend the ^a / ^x possibilities to dates, hex, alphabets, markdown headers
+	{
+		"monaqa/dial.nvim",
+		config = function()
+			local augend = require("dial.augend")
+			require("dial.config").augends:register_group({
+				-- default augends used when no group name is specified
+				default = {
+					augend.integer.alias.decimal,
+					augend.integer.alias.hex,
+					augend.date.alias["%Y/%m/%d"],
+					augend.date.alias["%Y-%m-%d"],
+					augend.date.alias["%m/%d"],
+					augend.date.alias["%H:%M:%S"],
+					augend.date.alias["%H:%M"],
+					augend.constant.alias.de_weekday_full,
+					augend.constant.alias.de_weekday,
+					augend.constant.alias.bool,
+					augend.semver.alias.semver,
+					augend.constant.alias.Alpha,
+					augend.constant.alias.alpha,
+					augend.hexcolor.new({ case = "lower" }),
+					augend.constant.new({
+						elements = { "and", "or" },
+						word = true, -- if false, "sand" is incremented into "sor", "doctor" into "doctand", etc.
+						cyclic = true, -- "or" is incremented into "and".
+					}),
+					augend.constant.new({
+						elements = { "&&", "||" },
+						word = false,
+						cyclic = true,
+					}),
+				},
+			})
+		end,
+		event = "VeryLazy",
+	},
+}

nvim/.config/nvim/lua/plugins/filebrowsers.lua

@@ -0,0 +1,18 @@
+return {
+	{
+		"vifm/vifm.vim",
+		config = function()
+			vim.g.loaded_netrw = 1
+			vim.g.loaded_netrwPlugin = 1
+			vim.g.vifm_replace_netrw = 1
+			vim.g.vifm_exec_args = '-c "set vifminfo=" -c "set statusline=" -c "only"'
+		end,
+		cmd = "Vifm",
+	}, -- integrate file manager
+	{
+		"nvim-tree/nvim-tree.lua", -- integrate file tree
+		config = true,
+		dependencies = { "nvim-tree/nvim-web-devicons", config = true },
+		cmd = "NvimTreeToggle",
+	},
+}

nvim/.config/nvim/lua/plugins/git.lua

@@ -0,0 +1,64 @@
+return {
+	{
+		"lewis6991/gitsigns.nvim", -- show vcs changes on left-hand gutter
+		event = "VeryLazy",
+		config = function()
+			require("gitsigns").setup({
+				numhl = true,
+				signcolumn = false,
+				on_attach = function(bufnr)
+					local gs = package.loaded.gitsigns
+
+					local function map(mode, l, r, opts)
+						opts = opts or {}
+						opts.buffer = bufnr
+						vim.keymap.set(mode, l, r, opts)
+					end
+
+					-- Navigation
+					map("n", "]h", function()
+						if vim.wo.diff then
+							return "]h"
+						end
+						vim.schedule(function()
+							gs.next_hunk()
+						end)
+						return "<Ignore>"
+					end, { expr = true })
+
+					map("n", "[h", function()
+						if vim.wo.diff then
+							return "[h"
+						end
+						vim.schedule(function()
+							gs.prev_hunk()
+						end)
+						return "<Ignore>"
+					end, { expr = true })
+
+					-- Actions
+					require("which-key").register({ ["<localleader>h"] = { name = "+git" } })
+					map({ "n", "v" }, "<localleader>hs", ":Gitsigns stage_hunk<CR>", { desc = "stage hunk" })
+					map({ "n", "v" }, "<localleader>hr", ":Gitsigns reset_hunk<CR>", { desc = "reset hunk" })
+					map("n", "<localleader>hS", gs.stage_buffer, { desc = "stage buffer" })
+					map("n", "<localleader>hu", gs.undo_stage_hunk, { desc = "undo stage hunk" })
+					map("n", "<localleader>hR", gs.reset_buffer, { desc = "reset buffer" })
+					map("n", "<localleader>hp", gs.preview_hunk, { desc = "preview hunk" })
+					map("n", "<localleader>hb", function()
+						gs.blame_line({ full = true })
+					end, { desc = "blame line" })
+					map("n", "<localleader>hB", gs.toggle_current_line_blame, { desc = "toggle blame" })
+					map("n", "<localleader>hd", gs.diffthis, { desc = "diffthis" })
+					map("n", "<localleader>hD", function()
+						gs.diffthis("~")
+					end, { desc = "diffbase" })
+					map("n", "<localleader>ht", gs.toggle_deleted, { desc = "toggle deleted" })
+
+					-- Text object
+					map({ "o", "x" }, "ih", ":<C-U>Gitsigns select_hunk<CR>")
+					map({ "o", "x" }, "ah", ":<C-U>Gitsigns select_hunk<CR>")
+				end,
+			})
+		end,
+	},
+}

nvim/.config/nvim/lua/plugins/ide.lua

@@ -0,0 +1,73 @@
+return {
+	-- vista-like outline view for code
+	{ "simrat39/symbols-outline.nvim", config = true, cmd = "SymbolsOutline" },
+	-- show a signature whenever editing a function or similar
+	{ "ray-x/lsp_signature.nvim", config = true, event = "VeryLazy" },
+	{
+		"junnplus/lsp-setup.nvim",
+		dependencies = {
+			"neovim/nvim-lspconfig",
+			{
+				"williamboman/mason.nvim",
+				cmd = {
+					"Mason",
+					"MasonInstall",
+					"MasonUninstall",
+					"MasonUninstallAll",
+					"MasonLog",
+					"MasonUpdate",
+				},
+				build = ":MasonUpdate",
+			},
+			{
+				"williamboman/mason-lspconfig.nvim",
+				cmd = { "LspInstall", "LspUninstall" },
+			},
+			{
+				"jose-elias-alvarez/null-ls.nvim",
+				dependencies = {
+					"nvim-lua/plenary.nvim",
+					"jay-babu/mason-null-ls.nvim",
+				},
+				event = "VeryLazy",
+			},
+		},
+		event = "BufReadPost",
+		config = function()
+			require("plugins.config.lsp")
+		end,
+	},
+	{
+		"hrsh7th/nvim-cmp",
+		branch = "main",
+		dependencies = {
+			"andersevenrud/cmp-tmux",
+			"cbarrete/completion-vcard",
+			"f3fora/cmp-spell",
+			"hrsh7th/cmp-nvim-lsp",
+			"hrsh7th/cmp-path",
+			"hrsh7th/cmp-buffer",
+			"hrsh7th/cmp-calc",
+			"hrsh7th/cmp-cmdline",
+			"hrsh7th/cmp-nvim-lua",
+			"dmitmel/cmp-digraphs",
+			"jc-doyle/cmp-pandoc-references",
+			"kdheepak/cmp-latex-symbols",
+			"lukas-reineke/cmp-rg",
+			"crispgm/cmp-beancount",
+			"ray-x/cmp-treesitter",
+			"saadparwaiz1/cmp_luasnip",
+			{
+				"L3MON4D3/LuaSnip",
+				dependencies = { "rafamadriz/friendly-snippets" },
+			},
+		},
+		config = function()
+			require("plugins.config.cmp")
+		end,
+		event = { "InsertEnter", "CmdlineEnter", "VeryLazy" },
+	},
+	-- loading animations for some LSP
+	{ "j-hui/fidget.nvim", config = true, tag = "legacy", event = "VeryLazy" },
+	-- a pretend-lsp for formatters and linters
+}

nvim/.config/nvim/lua/plugins/languages.lua

@@ -0,0 +1,5 @@
+return {
+	{ "edKotinsky/Arduino.nvim", ft = "arduino", config = true }, -- statusline
+	{ "euclidianAce/BetterLua.vim", ft = "lua" }, -- better syntax highlighting for lua
+	{ "aliou/bats.vim", ft = { "bash", "sh", "zsh", "bats" } }, -- enable syntax for bats shell-code testing library
+}

nvim/.config/nvim/lua/plugins/prose.lua

@@ -0,0 +1,56 @@
+local writing_ft = { "quarto", "pandoc", "markdown", "text", "tex" }
+
+return {
+	-- UI improvements
+	-- provide distraction free writing
+	{ "folke/zen-mode.nvim", config = true, event = "VeryLazy" },
+	-- provide even distraction free-er writing (lowlight paragraphs)
+	{ "folke/twilight.nvim", event = "VeryLazy" },
+	-- enable 'speed-reading' mode (bionic reading)
+	{
+		"JellyApple102/easyread.nvim",
+		config = true,
+		ft = writing_ft,
+		cmd = "EasyreadToggle",
+	},
+	{
+		"andrewferrier/wrapping.nvim",
+		config = function()
+			require("wrapping").setup({
+				create_keymappings = false,
+				notify_on_switch = false,
+			})
+		end,
+	},
+	-- generate an auto-updating html preview for md files
+	{
+		"iamcco/markdown-preview.nvim",
+		build = function()
+			vim.fn["mkdp#util#install"]()
+		end,
+		ft = writing_ft,
+	},
+
+	-- bring zettelkasten commands
+	{
+		"mickael-menu/zk-nvim",
+		config = function()
+			require("zk").setup({ picker = "telescope" })
+		end,
+	},
+	-- simple static markdown linking and link following using zettel IDs
+	{ "marty-oehme/zettelkasten.nvim", ft = writing_ft, event = "VeryLazy" },
+
+	-- syntax highlighting for markdown criticmarkup (comments, additions, ...)
+	{ "vim-pandoc/vim-criticmarkup", ft = writing_ft },
+	-- inline display of latex formulas
+	-- TODO always demands latex treesitter to be installed even if it is
+	-- TODO always turns softwrapped lines off on exiting insert mode
+	--{
+	--"jbyuki/nabla.nvim",
+	--ft = writing_ft,
+	--config = function()
+	--require("nabla").enable_virt({ autogen = true, silent = true })
+	--end,
+	--},
+}

nvim/.config/nvim/lua/plugins/telescope.lua

@@ -0,0 +1,77 @@
+return {
+	-- fuzzy matching
+	{
+		"nvim-telescope/telescope.nvim",
+		dependencies = {
+			"nvim-lua/popup.nvim",
+			"nvim-lua/plenary.nvim",
+			{ "nvim-telescope/telescope-fzf-native.nvim", build = "make" },
+		},
+		event = "VeryLazy",
+		cmd = "Telescope",
+		config = function()
+			-- Setup up telescope fuzzy finding settings
+			--
+			-- Makes use of optionally installed external programs to work fully:
+			-- rg (ripgrep) for in-text searches
+			-- fd for quicker directory structure searches
+			-- lsp for a variety of lsp queries
+			require("telescope").setup({
+				defaults = {
+					vimgrep_arguments = {
+						"rg",
+						"--ignore-vcs",
+						"--hidden",
+						"--color=never",
+						"--no-heading",
+						"--with-filename",
+						"--line-number",
+						"--column",
+						"--smart-case",
+					},
+					generic_sorter = require("mini.fuzzy").get_telescope_sorter,
+					-- Appearance
+					prompt_prefix = "  ",
+					selection_caret = "󰳟 ",
+					color_devicons = true,
+				},
+				pickers = {
+					buffers = { theme = "ivy" },
+					oldfiles = { theme = "ivy" },
+					find_files = {
+						theme = "dropdown",
+						-- nice minimal picker design
+						borderchars = {
+							{ "─", "│", "─", "│", "┌", "┐", "┘", "└" },
+							prompt = { "─", "│", " ", "│", "┌", "┐", "│", "│" },
+							results = {
+								"─",
+								"│",
+								"─",
+								"│",
+								"├",
+								"┤",
+								"┘",
+								"└",
+							},
+							preview = {
+								"─",
+								"│",
+								"─",
+								"│",
+								"┌",
+								"┐",
+								"┘",
+								"└",
+							},
+						},
+						width = 0.8,
+						previewer = false,
+						prompt_title = false,
+					},
+				},
+			})
+			require("telescope").load_extension("fzf")
+		end,
+	},
+}

nvim/.config/nvim/lua/plugins/treesitter.lua

@@ -0,0 +1,73 @@
+return {
+	{
+		"nvim-treesitter/nvim-treesitter",
+		build = ":TSUpdate",
+		config = function()
+			local rainbow = require("ts-rainbow")
+			require("nvim-treesitter.configs").setup({
+				-- one of "all", "maintained" (parsers with maintainers), or a list of languages
+				ensure_installed = "all",
+				highlight = {
+					enable = true,
+					disable = function(_, bufnr)
+						return vim.api.nvim_buf_line_count(bufnr) > 7000
+					end,
+				},
+				incremental_selection = { enable = true },
+				textobjects = { enable = true },
+				indent = { enable = true },
+				autotag = { enable = true },
+
+				-- enable rainbow brackets, needs p00f/nvim-ts-rainbow
+				rainbow = {
+					enable = true,
+					strategy = { rainbow.strategy.global },
+				},
+
+				-- for improved commentstrings, needs corresponding plugin
+				context_commentstring = {
+					enable = true,
+					enable_autocmd = false, -- since we run it as a hook from the mini.comment plugin
+				},
+				-- allows using . and ; to target treesitter branches
+				textsubjects = {
+					enable = true,
+					keymaps = {
+						["."] = "textsubjects-smart",
+						[";"] = "textsubjects-container-outer",
+					},
+				},
+			})
+		end,
+		event = "BufReadPost",
+		cmd = {
+			"TSBufDisable",
+			"TSBufEnable",
+			"TSBufToggle",
+			"TSDisable",
+			"TSEnable",
+			"TSToggle",
+			"TSInstall",
+			"TSInstallInfo",
+			"TSInstallSync",
+			"TSModuleInfo",
+			"TSUninstall",
+			"TSUpdate",
+			"TSUpdateSync",
+		},
+
+		-- rainbow brackets using treesitter
+		-- show current cursor context at top of buffer
+		-- improves commenting plugin above by using ts
+		dependencies = {
+			"https://gitlab.com/HiPhish/nvim-ts-rainbow2.git",
+			{ "romgrk/nvim-treesitter-context", config = true },
+			"JoosepAlviste/nvim-ts-context-commentstring",
+			{
+				"RRethy/nvim-treesitter-textsubjects",
+			},
+			"windwp/nvim-ts-autotag",
+		},
+	},
+	{ "nvim-treesitter/playground", cmd = "TSPlaygroundToggle" }, -- interactively view and query the treesitter tree
+}

nvim/.config/nvim/lua/plugins/ui.lua

@@ -0,0 +1,60 @@
+return {
+	-- statusline
+	{
+		"nvim-lualine/lualine.nvim",
+		requires = { "nvim-tree/nvim-web-devicons", config = true },
+		config = function()
+			require("plugins.config.lualine")
+		end,
+		event = "VeryLazy",
+	},
+	-- create a pretty pop-up notification
+	{
+		"rcarriga/nvim-notify",
+		config = function()
+			vim.notify = require("notify")
+		end,
+		event = "VeryLazy",
+	},
+	-- make all vim.ui interfaces prettyy
+	{ "stevearc/dressing.nvim", config = true, event = "VeryLazy" },
+
+	-- numbers to absolute for all buffers but the current which is relative
+	{ "jeffkreeftmeijer/vim-numbertoggle", event = "VeryLazy" },
+	-- auto-hiding colorcolumn
+	{
+		"m4xshen/smartcolumn.nvim",
+		event = "VeryLazy",
+		opts = {
+			colorcolumn = { "100" },
+			scope = "window",
+			disabled_filetypes = {
+				"help",
+				"text",
+				"markdown",
+				"NvimTree",
+				"lazy",
+				"mason",
+				"help",
+				"quarto",
+			},
+		},
+	},
+	-- display pretty colors when they are mentioned in buffer
+	{
+		"NvChad/nvim-colorizer.lua", -- color hex, named colors in the correct preview scheme
+		config = function()
+			require("colorizer").setup({
+				user_default_options = { mode = "virtualtext" },
+			})
+		end,
+		event = "VeryLazy",
+	},
+	{
+		"jiaoshijie/undotree",
+		dependencies = {
+			"nvim-lua/plenary.nvim",
+		},
+		config = true,		event = "VeryLazy",
+	},
+}

nvim/.config/nvim/lua/util/init.lua

@@ -0,0 +1,12 @@
+local T = {}
+
+-- from astronvim util function
+--- Check if a plugin is defined in lazy. Useful with lazy loading when a plugin is not necessarily loaded yet
+---@param plugin string The plugin to search for
+---@return boolean available # Whether the plugin is available
+function T.is_available(plugin)
+	local lazy_config_avail, lazy_config = pcall(require, "lazy.core.config")
+	return lazy_config_avail and lazy_config.plugins[plugin] ~= nil
+end
+
+return T

nvim/.config/nvim/plugin/personal/makescratch.vim

@@ -1,15 +0,0 @@
-" --[[ scratchpad.lua
-"
-" creates a 'scratch' buffer which is ephemeral --
-" it will disappear when vim closes, does not save to anything and does not
-" appear in the buffer list. Useful for e.g. jotting down quick notes and thoughts.
-"
-" If called with bang, will replace the current buffer with the scratch
-" window, otherwise opens a new split.
-"
-" The buffer, by default is set to the pandoc filetype.
-" This can be changed by setting the `g:scratchpad_ft` variable or the `b:scratchpad_ft`
-" variable to the intended filetype.
-" ]]--
-
-command! -nargs=? -bang ScratchPad :lua require("personal.scratchpad").create("<bang>","<args>")

nvim/.config/nvim/plugin/personal/searchnotes.vim

@@ -1,8 +0,0 @@
-function! SearchNotes()
-  let l:curpath=getcwd()
-  :execute(":cd " . g:wiki_root)
-  let l:texttofind=input("Search in Notes: ")
-  :execute(":CtrlSF " . l:texttofind)
-  :CtrlSFFocus
-  :execute(":cd " . l:curpath)
-endfunction

nvim/.config/nvim/plugin/thesaurus_query.vim

@@ -1,18 +0,0 @@
-" remove default keymappings
-let g:tq_map_keys=0
-
-" set custom mthesaur file if we have it
-if exists('$XDG_DATA_HOME')
-  let g:tq_mthesaur_file='$XDG_DATA_HOME' . '/nvim/thesaurus/mthesaur.txt'
-else
-  let g:tq_mthesaur_file=expand('~/.local/share/nvim/thesaurus/mthesaur.txt')
-endif
-
-" download if we don't
-if !filereadable(glob(g:tq_mthesaur_file))
-  echom 'No thesaurus file found, attempting to download in background...'
-  execute '!curl -fLo ' . expand(g:tq_mthesaur_file) . ' --create-dirs
-    \ http://www.gutenberg.org/files/3202/files/mthesaur.txt'
-endif
-
-let g:tq_language=['en', 'de']

nvim/.config/nvim/plugin/vifm.vim

@@ -1,4 +0,0 @@
-let g:loaded_netrw       = 1
-let g:loaded_netrwPlugin = 1
-let g:vifm_replace_netrw = 1
-let g:vifm_exec_args = '-c "set vifminfo=''''" -c "set statusline=''''" -c "only"'

writing/.config/pubs/pubsrc

@@ -0,0 +1,166 @@
+
+[main]
+
+# Where the pubs repository files (bibtex, metadata, notes) are located
+pubsdir = ~/documents/library
+
+# Where the documents files are located (default: $(pubsdir)/doc/)
+docsdir = ~/documents/library/doc
+
+# Specify if a document should be copied or moved in the docdir, or only
+# linked when adding a publication.
+doc_add = copy
+
+# the command to use when opening document files
+open_cmd = xdg-open
+
+# which editor to use when editing bibtex files.
+# if using a graphical editor, use the --wait or --block option, i.e.:
+# "atom --wait"
+# "kate --block"
+# If set to an empty string (default) pubs uses the value of the environment
+# variable $EDITOR.
+edit_cmd = ""
+
+# Which default extension to use when creating a note file.
+note_extension = md
+
+# How many authors to display when displaying a citation. If there are more
+# authors, only the first author is diplayed followed by 'et al.'.
+max_authors = 3
+
+# If true debug mode is on which means exceptions are not catched and
+# the full python stack is printed.
+debug = False
+
+# If true the citekey is normalized using the 'citekey_format' on adding new publications.
+normalize_citekey = False
+
+# String specifying how to format the citekey. All strings of
+# the form '{substitution:modifier}' and '{substitution}' will
+# be substituted with their appropriate values. The following
+# substitutions are used:
+#    author_last_name: last name of the first author
+#    year: year of publication
+#    short_title: first word of the title (excluding words such as "the", "an", ...)
+# modifiers:
+#    l: converts the text to lowercase
+#    u: converts the text to uppercase
+# examples:
+#   {author_last_name:l}{year} generates 'yang2020'
+#   {author_last_name}{year}{short_title} generates 'Yang2020Towards'
+#   {author_last_name:l}{year}{short_title:l} generates 'yang2020towards'
+#   {author_last_name:u}{year} generates 'YANG2020'
+#
+citekey_format = {author_last_name}{year}
+
+# which bibliographic fields to exclude from bibtex files. By default, none.
+# Please note that excluding critical fields such as `title` or `author`
+# will break many commands of pubs.
+exclude_bibtex_fields = ,
+
+[formating]
+
+# Enable bold formatting, if the terminal supports it.
+bold = True
+
+# Enable italics, if the terminal supports it.
+italics = True
+
+# Enable colors, if the terminal supports it.
+color = True
+
+
+[theme]
+
+# Here you can define the color theme used by pubs, if enabled in the
+# 'formating' section. Predefined theme are available at:
+# https://github.com/pubs/pubs/blob/master/extra/themes.md
+
+# Available colors are: 'black', 'red', 'green', 'yellow', 'blue', 'purple',
+# 'cyan', and 'grey'. Bold colors are available by prefixing 'b' in front of
+# the color name ('bblack', 'bred', etc.), italic colors by prefixing 'i',
+# and bold italic by prefixing 'bi'. Finally, 'bold', 'italic' and
+# 'bolditalic' can be used to apply formatting without changing the color.
+# For no color, use an empty string ''
+
+# messages
+ok = green
+warning = yellow
+error = red
+
+# ui elements
+filepath = bold
+citekey = purple
+tag = cyan
+
+# bibliographic fields
+author = bold
+title = ""
+publisher = ""
+year = bold
+volume = bold
+pages = ""
+
+
+[plugins]
+# Comma-separated list of the plugins to load.
+# Currently pubs comes with built-in plugins alias and git.
+active = alias,git
+
+[[alias]]
+# new subcommands can be defined, e.g.:
+# print = open --with lp
+# evince = open --with evince
+
+# shell commands can also be defined, by prefixing them with a bang `!`, e.g:
+# count = !pubs list -k | wc -l
+
+# aliases can also be defined with descriptions using the following configobj
+# subsectioning.  NOTE: any aliases defined this way should come after all other
+# aliases, otherwise simple aliases will be ignored.
+# [[[count]]]
+# command = !pubs list -k | wc -l
+# description = lists number of pubs in repo
+# new subcommands can be defined, e.g.:
+# print = open --with lp
+# evince = open --with evince
+
+# shell commands can also be defined, by prefixing them with a bang `!`, e.g:
+# count = !pubs list -k | wc -l
+
+# aliases can also be defined with descriptions using the following configobj
+# subsectioning.  NOTE: any aliases defined this way should come after all other
+# aliases, otherwise simple aliases will be ignored.
+# [[[count]]]
+# command = !pubs list -k | wc -l
+# description = lists number of pubs in repo
+
+# To use commas in the description, wrap them in a "" string. For example:
+# description = "lists number of pubs in repo, greets the user afterward"
+
+[[git]]
+# The git plugin will commit changes to the repository in a git repository
+# created at the root of the pubs directory. All detected changes will be
+# commited every time a change is made by a pubs command.
+# The plugin also propose the `pubs git` subcommand, to directly send git
+# commands to the pubs repository. Therefore, `pubs git status` is equivalent
+# to `git -C <pubsdir> status`, with the `-C` flag instructing
+# to invoke git as if the current directory was <pubsdir>. Note that a
+# limitation of the subcommand is that you cannot use git commands with the
+# `-c` option (pubs will interpret it first.)
+
+# if False, will display git output when automatic commit are made.
+# Invocation of `pubs git` will always have output displayed.
+quiet = True
+# if True, git will not automatically commit changes
+manual = False
+# if True, color will be conserved from git output (this add `-c color:always`
+# to the git invocation).
+force_color = True
+
+
+[internal]
+# The version of this configuration file. Do not edit.
+version = 0.9.0
+

writing/.config/sh/alias.d/pubs.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+pubs() {
+    command pubs --config "$XDG_CONFIG_HOME/pubs/pubsrc" "${@}"
+    if [ -f "$BIBFILE" ]; then
+        command pubs export > "$BIBFILE"
+    fi
+}