2026-01 updates

.config/nvim/lua/plugins/accelerated-jk.lua

@@ -1,7 +1,7 @@
 -- speeds up vertical navigation with j and k
 return {
   {
-    "rhysd/accelerated-jk",
+    "rainbowhxch/accelerated-jk.nvim",
     keys = {
       { "j", "<Plug>(accelerated_jk_gj)" },
       { "k", "<Plug>(accelerated_jk_gk)" },

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

@@ -20,6 +20,8 @@ return {
         python = { "ruff", "black" },
         bash = { "shfmt" },
         sh = { "shfmt" },
+        snakemake = { "snakefmt" },
+        markdown = { "markdownlint" },
       },
       formatters = {
         shfmt = {

.config/nvim/lua/plugins/nvim-tree.lua

@@ -6,7 +6,32 @@ return {
     -- don't lazy load; otherwise, opening a directory as first buffer doesn't trigger it.
     lazy = false,
 
-    config = true,
+    config = function()
+      require("nvim-tree").setup({
+        on_attach = function(bufnr)
+          local api = require("nvim-tree.api")
+
+          api.config.mappings.default_on_attach(bufnr)
+
+          local function git_add()
+            local node = api.tree.get_node_under_cursor()
+            if node and node.absolute_path then
+              vim.cmd("Git add " .. vim.fn.fnameescape(node.absolute_path))
+              api.tree.reload()
+            end
+          end
+            local function git_unstage()
+          local node = api.tree.get_node_under_cursor()
+          if node and node.absolute_path then
+              vim.cmd("Git restore --staged " .. vim.fn.fnameescape(node.absolute_path))
+            api.tree.reload()
+          end
+        end
+        vim.keymap.set("n", "ga", git_add, { buffer = bufnr, desc = "Git Add" })
+        vim.keymap.set("n", "gu", git_unstage, { buffer = bufnr, desc = "Git Unstage" })
+        end,
+        })
+    end,
     keys = {
       { "<leader>fb", "<cmd>NvimTreeToggle<CR>", desc = "[f]ile [b]rowser toggle" },
     },

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

@@ -0,0 +1,12 @@
+return {
+  {
+    "snakemake/snakemake",
+    ft = "snakemake",
+    config = function(plugin)
+      vim.opt.rtp:append(plugin.dir .. "/misc/vim")
+    end,
+    init = function(plugin)
+      require("lazy.core.loader").ftdetect(plugin.dir .. "/misc/vim")
+    end,
+  },
+}

docs/changelog.rst

@@ -1,6 +1,18 @@
 Changelog
 =========
 
+2026-01-17
+----------
+
+**vim**
+
+- Add snakemake formatter
+- Add snakemake filetype plugin
+- Add markdown linter
+- Use updated accelerated-jk repo
+- Support adding files to git from within nvim-tree (:kbd:`ga`) or unstaging (:kbd:`gu`)
+
+
 2025-11-21
 ----------
 

docs/nvim-plugins.rst

@@ -50,9 +50,10 @@ load plugins when they're needed. See :ref:`nvim-lua` for my rationale on that.
 Because of how frequently nvim changes, each plugin section below has
 a changelog. Since I have reorganized files over the years, the changelogs show
 the *mention* of a plugin in a commit message, in a filename, or as part of the
-changeset of a commit in an attempt to catch all of the changes. This may be
-a little overzealous (for example the ``trouble`` plugin picks up commits
-related to troubleshooting) but I've opted to err on the side of completeness.
+changeset of a commit. Checking all of these things is an attempt to catch all
+of the changes. This may be a little overzealous (for example the ``trouble``
+plugin picks up commits related to troubleshooting) but I've opted to err on
+the side of completeness.
 
 Plugin list
 -----------
@@ -633,6 +634,13 @@ Other useful things you can do with Telescope:
       - Opens file in editor, expands directory to show contents, or collapses
         open directory
 
+    * - :kbd:`ga` (within browser)
+      - Add file to git. Useful when you have fugitive also open, and want to
+        add a file from an as-yet-untracked directory
+
+    * - :kbd:`gu` (within browser)
+      - Unstage file to git. Useful when you have fugitive also open
+
 The window-switching shortcuts :kbd:`<leader>w` and :kbd:`<leader>q` (move to
 windows left and right respectively; see :ref:`toggleterm_ref`) also work.