.github/workflows/check.yml

@@ -5,20 +5,12 @@ on:
     paths:
       - 'flake.lock'
       - 'flake.nix'
-      - 'modules/**'
+      - 'modules'
-      - 'plugin/**'
-      - 'lua/**'
-      - 'overlays/**'
-      - 'ftplugin/**'
   pull_request:
     paths:
       - 'flake.lock'
       - 'flake.nix'
-      - 'modules/**'
+      - 'modules'
-      - 'plugin/**'
-      - 'lua/**'
-      - 'overlays/**'
-      - 'ftplugin/**'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -43,5 +35,5 @@ jobs:
         authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
         extraPullNames: rstats-on-nix, nix-community    
     - run: nix build
-    - run: nix develop -c echo ok
+    - run: nix develop
     - run: nix flake check

.kilo/plans/1784851829193-codecompanion-revamp.md

@@ -1,85 +0,0 @@
-# CodeCompanion Revamp Plan
-
-## Context
-
-- Current: CodeCompanion **19.18.0** via nixpkgs `vimPlugins.codecompanion-nvim` (nixpkgs input lastModified ~2026-05-15).
-- Latest: **19.20.0**. Key changes since 19.18.0:
-  - v19.19.0: `claude-sonnet-5` support, async/dynamic model fetching, copilot `top_p` fixes, inline orphaned-keymap fix, background command deregistration.
-  - v19.20.0: `gemini_interactions` adapter, PDF support for http adapters (`/file` on Anthropic/Copilot/OpenAI/OpenRouter), env vars from files, prompt-library items auto-receive default rule groups, copilot schema options removed.
-- **Bug in current setup:** config sets `model = "claude-sonnet-5"` but 19.18.0 predates its support; the model name may not resolve. The nixpkgs bump fixes this.
-- Files involved:
-  - `plugin/24_completion.lua` — `get_codecompanion_config()`, setup, blink integration.
-  - `plugin/10_keymap.lua` — `<leader>a*` keymaps (lines 69–84, contains duplicates/commented cruft).
-  - `overlays/plugins.nix` — codecompanion overlay (nvimSkipModules); likely unchanged.
-  - `modules/module/specs/plugins.nix` — plugin spec; unchanged.
-
-## Decisions (confirmed with user)
-
-1. **Version bump:** `nix flake update nixpkgs` (accepts wider plugin bump; do NOT override src).
-2. **Adopt:** agent-mode keymaps, one workflow prompt, minor slash-command config (`/share` token). **No MCP.**
-3. **Models:** `claude-sonnet-5` (copilot) for **chat only**; cheaper copilot model for **inline** and **background** (title generation) — use `gpt-5-mini` as placeholder; verify exact model id via `ga` model picker in a chat buffer after the bump and adjust.
-4. **Codex (ChatGPT Edu) = heavy agent lane.** Copilot stays the default chat adapter; Codex ACP is launched explicitly for heavy autonomous tasks. Auth via ChatGPT login only (no API key) — user's existing `auth_method = "chatgpt"` is correct per the v19.20.0 adapter source (`"openai-api-key"|"codex-api-key"|"chatgpt"`; the docs page comment `"chat-gpt"` is stale).
-
-## Tasks
-
-1. **Bump nixpkgs**
-   - Run `nix flake update nixpkgs`.
-   - Verify: `nix eval --raw nixpkgs#vimPlugins.codecompanion-nvim.version` reports ≥ 19.20.0.
-   - Rebuild the wrapped Neovim per this repo's normal build (`nix build` / the repo's usual package target) and smoke-test that the editor starts.
-
-2. **`plugin/24_completion.lua` — `get_codecompanion_config()`**
-   - Keep `interactions.chat.adapter = { name = "copilot", model = "claude-sonnet-5" }`.
-   - Change `interactions.inline.adapter` to `{ name = "copilot", model = "gpt-5-mini" }` (cheap/fast).
-   - Add a background adapter so title generation doesn't use Sonnet: set the background chat adapter to copilot/`gpt-5-mini` (config lives under `interactions.background.chat`; confirm exact key against `:h codecompanion` / `:checkhealth codecompanion` after the bump — the docs page "Generating Titles" says an adapter must be configured for background interactions).
-   - Keep existing context_management, rules, display, shared keymaps unchanged.
-   - Add `interactions.chat.slash_commands["share"].opts.token = os.getenv("GITHUB_GIST_TOKEN")`.
-   - **Prompt library additions** (keep `expert`, `fixer`, `suggest`):
-     - `["agent"]`: interaction "chat", alias `agent`, first user prompt starts with `@{agent}` plus selected code block, so Copilot/Claude gets the file-editing tool group (read_file, insert_edit_into_file, grep_search, run_command, etc., with approvals).
-     - `["tdd"]` (name flexible): interaction "chat", `opts = { is_workflow = true, alias = "tdd" }` — 3-stage workflow: (1) plan/understand `#buffer`, (2) `@{agent}` implement, (3) `@{run_command}` run the test suite (leverages run_command's test-flag for agentic workflows).
-
-3. **`plugin/10_keymap.lua` — clean up + add**
-   - Remove duplicated/commented lines (70–71, 77, 81).
-   - Add:
-     - `nmap_leader("aa", "<cmd>CodeCompanionChat<CR>", "Agent chat (use @{agent})")` or directly `<cmd>CodeCompanion /agent<CR>`.
-     - `xmap_leader("aa", "<cmd>CodeCompanion /agent<CR>", "Agent on selection")`.
-     - `nmap_leader("aw", "<cmd>CodeCompanion /tdd<CR>", "Workflow: plan→implement→test")`.
-     - `nmap_leader("aC", "<cmd>CodeCompanion /compact<CR>", "Compact chat")` (verify `<leader>aC` doesn't clash).
-   - Keep existing mappings unchanged.
-
-4. **No changes** to `overlays/plugins.nix` or `modules/module/specs/plugins.nix` unless the new version introduces new lazy-module load failures (re-run the build's check phase; `doCheck = false` is already set on the spec entry).
-
-5. **Codex ACP lane (ChatGPT Edu)**
-   - **Resolved prerequisite:** user has installed `codex-acp` at `~/.nix-profile/bin/codex-acp` (verified on PATH 2026-07-24). The preset adapter's default command (`codex-acp`) now works as-is — **no `commands` override in the Lua config**. Fallback only if the binary misbehaves: override with `commands = { default = { "codex", "acp" } }` (requires the codex CLI's built-in `acp` subcommand; verify with `codex acp --help`).
-   - **Config change (small):** none strictly required — the existing `extend("codex", { defaults = { auth_method = "chatgpt" } })` block in `plugin/24_completion.lua` is correct. Keep it.
-   - Auth: prereq is an active `codex login` session with the ChatGPT Edu account (`~/.codex/auth.json` exists — user confirms validity; if expired, re-run `codex login`, browser/ChatGPT-app flow, no API key).
-   - Keep codex on-demand (do NOT make it the default chat adapter):
-     - Keep `<leader>ak` (`:CodeCompanionChat adapter=codex`).
-     - Add comment documenting ACP-only slash commands for this lane: `/resume` (restore past codex session, fresh chat only), `/mode` (switch agent mode), `/command`, `/acp_session_options`, plus `\`-triggered ACP command completion in the chat buffer.
-   - Do not set a default codex model in config; pick per-session via `ga` / `/acp_session_options` (avoids hardcoding model ids that change with the Edu plan).
-   - PATH note: Neovim must inherit a PATH containing `~/.nix-profile/bin` so the spawned `codex-acp` resolves — true when nvim is launched from the user's normal shell; call it out if validation fails with "command not found".
-
-6. **Docs/habit notes** (add as comment block above the codecompanion setup, no separate docs file): `/compact`, `/fork`, `/symbols`, `/share`, `/resume`+`/mode` (codex ACP), `gm` (btw), `gty` (YOLO), `gba`/`gbd` (buffer sync), `gd` (debug window).
-
-## Validation
-
-- `nix flake update nixpkgs` then repo build succeeds.
-- In Neovim: `:checkhealth codecompanion` clean.
-- `:CodeCompanionChat`, press `ga` → copilot adapter lists `claude-sonnet-5`; send a trivial message and confirm response + auto title generation.
-- In chat: type `@` → completion shows `agent`, `files`, `memory`, etc.; run `@{agent}` task on a scratch repo and confirm the approval prompt flow works.
-- `:CodeCompanion /tdd` starts the workflow stages in order.
-- Inline: visual-select code, `:CodeCompanion` prompt → confirm diff shows and `ga`/`gr` accept/reject still work on the cheap model.
-- `:CodeCompanion /share` prompts/errors sensibly if `GITHUB_GIST_TOKEN` unset.
-- **Codex lane:** `<leader>ak` opens a chat with the codex ACP adapter; the spawned `codex-acp` process initializes without auth errors (ChatGPT method), a trivial prompt gets a response, and `/mode` lists codex session modes. If it fails with command-not-found, check that Neovim inherited `~/.nix-profile/bin` in PATH (`:echo $PATH` inside nvim).
-
-## Risks
-
-- `nix flake update nixpkgs` bumps **all** vimPlugins and Neovim itself; other plugins may break. If the blast radius is too large, fall back to overriding codecompanion `src` to tag `v19.20.0` in `overlays/plugins.nix` (fetchFromGitHub, `doCheck = false`).
-- Model ids (`claude-sonnet-5`, `gpt-5-mini`) must match the copilot adapter's choices post-bump; verify via `ga` picker and adjust literals.
-- `gpt-5-mini` may not support tool use on copilot — fine, since inline/background don't use tools.
-- `codex-acp` lives in the user's nix profile (outside this flake). If the profile is rebuilt/removed, the codex lane breaks — long-term consider adding `codex-acp` to this flake's runtime deps so it's pinned with the rest of the setup (optional follow-up, not required now).
-- ChatGPT Edu accounts authenticate codex via browser/ChatGPT-app login; token expiry will surface as ACP auth errors → re-run `codex login`.
-
-## Out of scope
-
-- MCP server integration.
-- Custom rules parsers, custom tools, extensions (mcphub/history/vectorcode).

.kilo/plans/1784858731550-nix-neovim-review.md

@@ -1,191 +0,0 @@
-# Neovim + Nix setup review
-
-Scope: `flake.nix`, `overlays/`, `modules/`, `plugin/*.lua`, `lua/*`, `ftplugin/*`, CI/workflows, and cross-check against the pinned versions in `flake.lock` (nixpkgs weekly `241313f4`).
-
-## Pinned package versions (from current lock)
-- neovim `0.12.2`
-- blink-cmp `1.10.2`
-- codecompanion-nvim `19.13.0`
-- nvim-treesitter `0.10.0-unstable-2026-04-03` (main-branch rewrite)
-- nvim-treesitter-textobjects `0-unstable-2026-04-07` (main-branch rewrite)
-- copilot-lua `2.0.3`
-- render-markdown-nvim `8.12.0-unstable-2026-05-07`
-- zk-nvim `0.4.7-unstable-2026-03-13`
-- mini.nvim `0.17.0-unstable-2026-05-12`
-- quarto-nvim `2.1.0`
-- otter-nvim `2.14.5`
-- lspconfig `2.9.0`
-
----
-
-## CRITICAL: Treesitter is currently non-functional
-
-### Finding
-The nixpkgs `nvim-treesitter` package is the **main-branch rewrite** — there is no `lua/nvim-treesitter/configs.lua`. The whole module in `plugin/20_startup.lua` lines 212-294 is dead code:
-
-```lua
-local ok_configs, configs = pcall(require, "nvim-treesitter.configs")  -- fails
-```
-
-The working tree already removed the fallback `vim.treesitter.start()` FileType autocmd (the "fixed treesitter" commit deleted it). Net result: **no treesitter highlighting, indentexpr, foldexpr, or textobjects are configured**.
-
-### Impact
-- Syntax highlighting falls back to Neovim's regex-only engine.
-- All textobject keymaps (`]a`, `[a`, `]f`, `[f`, `]e`/`[e`, `<leader>x`/`X`, lsp_interop `<leader>lm`) are inert.
-- `foldexpr`/`indentexpr` based folding does nothing.
-
-### Fix direction
-Rewrite `plugin/20_startup.lua` for main-branch API:
-1. FileType autocmd → `vim.treesitter.start()` (and optionally `indentexpr`/`foldexpr`).
-2. `require("nvim-treesitter-textobjects").setup({ move = { set_jumps = true } })` + explicit keymaps using `move.goto_next_start(query, "textobjects")` and `swap.swap_next(...)`.
-3. The non-Nix `ensure_installed` block should set `opts.ensure_installed` BEFORE the filter (line 278 reads it before line 286 defines it).
-
-Also remove duplicate `vim.treesitter.language.register("markdown", ...)` between `plugin/20_startup.lua` and `plugin/21_datascience.lua`.
-
----
-
-## CodeCompanion version mismatch
-
-### Finding
-Config targets features absent in `19.13.0` (present only in `≥19.19.0`/main):
-
-| Config usage | Present in 19.13? | Present in main (`v19.20.0`) |
-|---|---|---|
-| `interactions.chat.opts.context_management.editing` | No (flat `trigger`/`enabled` only) | Yes |
-| `interactions.chat.opts.context_management.compaction` | No | Yes |
-| `<leader>aC` requiring `codecompanion.interactions.chat.context_management.compaction` | **RUNTIME ERROR** | Works |
-| `slash_commands.share` (`opts.token = ...`) | No (absent from defaults) | Yes |
-| `adapters.acp.codex.defaults.auth_method = "chatgpt"` | Yes | Yes |
-| `interactions.chat.adapter = { name = ..., model = ... }` table form | Yes | Yes |
-
-### Risk
-On today's lock (`19.13.0`): `/share` is inert, compaction-only keymap throws module-not-found, and `editing`/`compaction` tuning is silently ignored. On `≥19.19.0`/main: everything works.
-
-### Decision needed (BLOCKING)
-Choose **exactly one**:
-
-- **A — Upgrade the plugin pin** (`overlays/plugins.nix` fetch to `v19.20.0` or `main`, bump the lock, and keep the current config). Riskiest change but matches what the config is written for.
-- **B — Downgrade config call sites** to match `19.13.0`: remove `slash_commands.share`, remove `editing`/`compaction` keys (or collapse to flat `trigger: 0.75`), remove or gate `<leader>aC` on "newer" version.
-- **C — Version-gate the config**: keep current code, read the installed version at startup and skip the new features when < 19.19.
-
-I recommend A (the config clearly intends to track upstream main-ish behavior; `nix flake update` already bumped it to `19.18.0` in a prior session and you only reverted because the nightly was still too old — `v19.20.0` is now available).
-
----
-
-## DEAD / DUPLICATE code
-
-- `plugin/20_startup.lua` — the entire `configs.setup(opts)` block is dead (see Treesitter finding above).
-- `plugin/10_keymap.lua`:
-  - `nmap_leader('od', '<Cmd>Neogen<CR>', ...)` — `neogen` plugin is **not shipped** in `specs/plugins.nix`. Mapping errors on press.
-  - `nmap_leader('fp', '<Cmd>Pick projects<CR>', ...)` — `MiniExtra.pickers.projects` doesn't exist in mini.extra; would error.
-  - `nmap_leader('oS', '<Cmd>lua Config.insert_section()<CR>', ...)` — `Config.insert_section` is never defined.
-  - `vim.lsp.buf.definition()` is bound to `grd`; Neovim 0.11+ defaults include `gr` aliases. Cosmetic, but `]d`/`[d` exist on modern LSP config and would be more idiomatic.
-- `plugin/23_editor.lua`:
-  - `my_styler` formatter (calls `R -s -e styler::...`) is defined but never referenced — dead.
-- `plugin/24_completion.lua`:
-  - `providers.cmp_r` is defined in the blink source list but never enabled in `default` or `per_filetype`; inert.
-  - `BLINK_VERSION = "v1.4.1"` — only consulted in the non-Nix install path; nixpkgs is `1.10.2`. Pin it to current or drop.
-  - `get_blink_fuzzy_setting().prebuilt_binary = { force_version = BLINK_VERSION }` — singular key is wrong; blink option is `fuzzy.prebuilt_binaries` (plural). Being skipped in-Nix anyway, but still wrong key.
-- `modules/module/specs/plugins.nix` — `specs.utils-lazy` ships `nvim-dap*` and `nvim-lint` but there is zero config/tooling that references them in this repo.
-- `ftplugin/quarto.lua`:
-  - Second top-level `require('quarto').setup()` with **no args** runs _after_ `21_datascience.lua`'s setup and **resets** it to defaults (no `lspFeatures`, no `codeRunner`).
-  - Top-level `require('quarto')` at FileType load also crashes if the quarto plugin isn't installed (e.g. cats off and a `.qmd`/`.quarto` file is opened): Neovim detects `quarto` ft natively in 0.10+.
-- `plugin/00_options.lua`:
-  - Lines 146-163: two back-to-back FileType autocmds that both remove `r`/`o` from `formatoptions`. The second references an undefined `augroup` variable (nil → autocmd is global, happens to still work).
-
----
-
-## STALE / WRONG options
-
-- `plugin/10_keymap.lua` line 174:
-  ```lua
-  require("conform").format({ lsp_fallback = true })
-  ```
-  `lsp_fallback` is the **deprecated** boolean form of `conform.nvim`; should be `lsp_format = "fallback"` (the form already used in `plugin/23_editor.lua` and `ftplugin/python.lua`). In newer conform this may warn or error.
-- `ftplugin/quarto.lua`:
-  - Sets `<Plug>RDSendLine` and R-style keymaps on _all_ quarto buffers, including Python/Julia chunks. This collides with quarto-runner mappings set in `21_datascience.lua`. Should gate on `vim.bo.filetype == "r"` (the ftplugin already imports quarto.runner for python, but the R keys leak).
-- `.github/dependapot.yml` — filename typo. GitHub expects `dependabot.yml`; Dependabot won't run.
-- `.github/workflows/check.yml`:
-  - `nix develop` without a `-c` command just launches an interactive shell. In CI it does nothing useful (or hangs). Replace with `nix develop -c echo ok` or drop.
-  - Path filter `'modules'` only matches the root directory itself; should be `modules/**` (or `'modules/**'`).
-  - Changing `plugin/`, `lua/`, `overlays/`, `ftplugin/`, etc. does **not** trigger CI.
-- `flake.nix` / `.envrc` shellHook:
-  ```sh
-  export R_LIBS_SITE=$(strings "$(command -v R)" | grep -oP '/nix/store/[^:]+/library' ...)
-  ```
-  `grep -oP` (PCRE) is **not available in macOS BSD grep**. On `aarch64-darwin` this silently fails → `R_LIBS_SITE` is empty. Either depend on `ripgrep` regex (`strings ... | rg -o '...'`) or use `gsed` (GNU sed).
-- `overlays/plugins.nix` — `zk-nvim` skip list contains `zk.pickers.fzf_lua`; current zk-nvim package likely doesn't load that regardless, but harmless.
-- `modules/module/settings/core.nix` — `config.settings.nvim_lua_env` references `lp.tiktoken_core` but `tiktoken_core` is **not in `catPkgs.general` or anywhere else** in these files. If there's an extra Lua/tiktoken module, fine; otherwise this option is placeholder dead code.
-- `modules/module/settings/hosts.nix` — host `m` (marimo) is defined with `enable = false` but also configured with `package`, `argv0`, `addFlag`. Dead block.
-
----
-
-## PORTABILITY / DARWIN issues
-
-- Shell hook `grep -oP` (above) fails on macOS.
-- `mkdir -p "$R_LIBS_USER"` fine; but `command -v R` on macOS returns the wrapper; the wrapper path injection still works.
-
----
-
-## DEAD WEIGHT (shipped but unused)
-
-- `catPkgs.r` includes `pkgs.rnvimserver` — `rnvimserver` is needed by R.nvim only when using the _socket_ transport; `21_datascience.lua` only uses vim-slime. Acceptable, but `rnvimserver` adds to build time. Include if you actually use it? Currently not used.
-- `specs.utils-lazy` ships `nvim-dap`, `nvim-dap-ui`, `nvim-dap-virtual-text`, `nvim-lint` — none of these are referenced anywhere in `plugin/` or `lua/`. Consider moving them to a devShell-only cat, or drop them.
-- `.gitignore` `*.R` — prevents tracking any new `.R` files. `tests/test.R` is already committed so it isn't actively harmful, but it's surprising for a repo whose default cats include R.
-- `.commandcode/` dir is listed in `.gitignore` but is in the worktree; fine, but worth cleaning up if it's an artifact.
-
----
-
-## IMPROVEMENTS given updated packages
-
-- `catPkgs.markdown` — add `marksman` (it's the LSP used by `render-markdown.nvim` wiki links and configured in LSP). Same binary is needed by `render-markdown` for wiki link ISP.
-- `vim.lsp.enable` servers configured but binaries missing in PATH:
-  - `marksman` (LSP + render-markdown wiki integration).
-  - `r_ls` (new R language server — package name in nixpkgs is likely `r-languageserver` or `r_ls`; current `catPkgs.r` doesn't ship either).
-  - `clangd` — not required for this data-science setup; either drop or add to `external`.
-  - `julials` — require `LanguageServer.jl` in `settings.lang_packages.julia` for it to be useful.
-- `blink.cmp` is `1.10.2` but config pins `BLINK_VERSION = "v1.4.1"` for the non-Nix path. Either drop the `BLINK_VERSION` constant (let MiniDeps track HEAD or the tag pinned in flake) or update it to `v1.10.2`.
-- `conform.nvim` already uses `lsp_format = "fallback"` in `23_editor.lua` and `ftplugin/python.lua`, but `10_keymap.lua` still calls the deprecated `lsp_fallback = true`. Align to `lsp_format = "fallback"`.
-- `.github/workflows/check.yml` — add path filters for `plugin/**`, `lua/**`, `overlays/**`, `ftplugin/**`, `modules/**`.
-- `tests/init.lua` smoke-test and `tests/test.R` are present but **not wired into `nix flake check`**. Add a trivial check that runs `lua tests/init.lua` via `nix-shell -A ...`.
-
----
-
-## CONFLICTS
-
-- `<leader>up` (terminal bracketed paste toggle in `10_keymap.lua`) conflicts with `mini.basics.mappings.option_toggle_prefix = "<leader>u"` (paste toggle), which is set up later in `20_startup.lua` via `now()`. Result: the user's `<leader>up` mapping gets overwritten. Portable workaround: remap to `<leader>tp` (terminal namespace) and keep `<leader>tb` as alternative — both already mapped in 10_keymap.
-- `ftplugin/quarto.lua` resets quarto-nvim config (kills `lspFeatures`/`codeRunner` set in `21_datascience.lua`) and injects R plug mappings into non-R quarto chunks.
-
----
-
-## CLEAN summary for implementer
-
-### Immediate (not version-dependent)
-1. Restore treesitter highlighting + textobjects in `plugin/20_startup.lua` using main-branch API.
-2. Remove duplicate `vim.treesitter.language.register` in `21_datascience.lua`.
-3. Fix `plugin/10_keymap.lua`: remove/resolve `Neogen`, `Pick projects`, `Config.insert_section` dangling mappings.
-4. Replace deprecated `lsp_fallback = true` with `lsp_format = "fallback"` in `plugin/10_keymap.lua`.
-5. Gate `ftplugin/quarto.lua` to not reset config and to not leak R keys into non-R chunks; guard against missing `quarto` plugin.
-6. Remove duplicate `formatoptions` autocmds (or at least dedupe).
-7. Dedupe `RNVIM_COMPLDIR` / `TMPDIR` setup (do it in one place).
-8. Rename `.github/dependapot.yml` to `.github/dependabot.yml`.
-9. Remove or gate dead host `m` in `hosts.nix`.
-10. Remove unused `rsplit`? no, irrelevant.
-11. Add `marksman` to `catPkgs.markdown` and remove orphan LSP entries or ship the binaries.
-12. Remove dead `conform` formatter `my_styler` and dead blink `cmp_r` provider, or wire them up.
-
-### Version-dependent (BLOCKED)
-- **Reset the CodeCompanion version decision**: either pin to `v19.20.0` (keep config, fix `slash_commands.share`, drop the `<leader>aC` compatibility shim, keep `editing`/`compaction`) OR downgrade config to match `19.13.0` (remove `share`, collapse `context_management`).
-
-### CI / packaging
-- Fix `nix develop` usage and path filters in `.github/workflows/check.yml`.
-- Replace `grep -oP` in `flake.nix` shellHook with portable `rg -o` or add `gnused` to `catPkgs.always` and use `gsed`.
-- Wire `tests/init.lua` into `flake check`.
-
-### Verification
-- `nix flake check` on both `aarch64-darwin` and `x86_64-linux`.
-- `nix build .#packages.<system>.default` succeeds (already does).
-- Start nvim, verify :TSContext works, treesitter highlighting is on, and `]f`/`[f` textobjects move.
-- Open a `.qmd` file with cats off → no ftplugin crash.
-- Confirm `<leader>up` still toggles bracketed paste.
-- Confirm `:Pick projects` and `:Neogen` and `Config.insert_section` no longer error (or are mapped to valid handlers).

flake.lock

@@ -7,11 +7,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1781337902,
+        "lastModified": 1776413584,
-        "narHash": "sha256-QjXxUvpOBbnlpSskBOZJ9nUbpYyFRD4cBo4s1aHniGs=",
+        "narHash": "sha256-xqqv46MTveuT4yJH2YihmbHGy5mdLnnLFDebVmUws/E=",
         "owner": "dwinkler1",
         "repo": "fran",
-        "rev": "30ab141871ede23b245a90afea58e076ef83b515",
+        "rev": "da09626e4dd8f0f57078b3a04e0443a8c20defa1",
         "type": "github"
       },
       "original": {
@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1784796856,
+        "lastModified": 1778869304,
-        "narHash": "sha256-wWFrV5/Qbm+lyt5x20E/bSbfJiGKMo4RCxZV8cl/WZI=",
+        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "e2587caef70cea85dd97d7daab492899902dbf5d",
+        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
         "type": "github"
       },
       "original": {
@@ -60,16 +60,16 @@
         "rnvimsrc": "rnvimsrc"
       },
       "locked": {
-        "lastModified": 1784867506,
+        "lastModified": 1781392459,
-        "narHash": "sha256-5zXVJLG7+Gi9sgb4Dn7P6O/ywQQxpvcjjoHSJXZEuVo=",
+        "narHash": "sha256-9CMG+trBd9AX7cWiGPrMr0eJwuZaql+pj2WVGyT417I=",
         "owner": "dwinkler1",
         "repo": "r_nvim_nix",
-        "rev": "1d26452e3c940153271fc57fbad0b295fcb0e04f",
+        "rev": "03d7872d7702db37ede41f3c6e4d4ce4c129e862",
         "type": "github"
       },
       "original": {
         "owner": "dwinkler1",
-        "ref": "v1.0.0",
+        "ref": "v0.99.5",
         "repo": "r_nvim_nix",
         "type": "github"
       }
@@ -93,16 +93,16 @@
     "rnvimsrc": {
       "flake": false,
       "locked": {
-        "lastModified": 1783264911,
+        "lastModified": 1780759435,
-        "narHash": "sha256-FywUL3mV2+kfu+rO6uUFyUv80EflbdgSkYuSnW965UE=",
+        "narHash": "sha256-VxgKMOP1hseQre3cas2dmMXZu4PVyl05INla2OdHTU4=",
         "owner": "R-nvim",
         "repo": "R.nvim",
-        "rev": "c56ebe0f8445e251673981c40ac2d74659ecd6ed",
+        "rev": "6ca306191531c3e3d501ee1609c84a5d29059386",
         "type": "github"
       },
       "original": {
         "owner": "R-nvim",
-        "ref": "v1.0.0",
+        "ref": "v0.99.5",
         "repo": "R.nvim",
         "type": "github"
       }
@@ -124,11 +124,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1782135443,
+        "lastModified": 1779297405,
-        "narHash": "sha256-vAmbArdCyjqpVW+37aCy/PMBOLIqukUXLQuEKLwUhA4=",
+        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "6e7f66fa2cdf4d63162580b438f7fcf87c28a46f",
+        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
         "type": "github"
       },
       "original": {

flake.nix

@@ -12,7 +12,7 @@
     rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs";
 
     r-nvim-nix = {
-      url = "github:dwinkler1/r_nvim_nix/v1.0.0";
+      url = "github:dwinkler1/r_nvim_nix/v0.99.5";
       inputs = {
         nixpkgs.follows = "rixpkgs";
       };
@@ -69,7 +69,7 @@
       ''
       + nixpkgs.lib.optionalString (config.cats.r or false) ''
         export R_HOME=$(R RHOME)
-        export R_LIBS_SITE=$(strings "$(command -v R)" | rg -o '/nix/store/[^:]+/library' | sort -u | paste -sd: -)
+        export R_LIBS_SITE=$(strings "$(command -v R)" | grep -oP '/nix/store/[^:]+/library' | sort -u | paste -sd: -)
         export R_LIBS_USER="$PWD/.r-libs"
         mkdir -p "$R_LIBS_USER"
       '';
@@ -224,23 +224,18 @@
             fi
             echo "Downstream override assertions passed" > $out
           '';
-        lua-test = pkgs.runCommand "lua-test" {
-          buildInputs = [ pkgs.neovim-unwrapped ];
-        } ''
-          nvim --headless -u NONE -c "set runtimepath+=${./.}" -l ${./tests/init.lua}
-          touch $out
-        '';
       }
     );
 
-    nixosModules.default = wrappers.lib.getInstallModule {
+    nixosModules.default = wrappers.lib.mkInstallModule {
       name = "vModule";
       value = module;
     };
 
-    homeModules.default = wrappers.lib.getInstallModule {
+    homeModules.default = wrappers.lib.mkInstallModule {
       name = "vModule";
       value = module;
+      loc = ["home" "packages"];
     };
   };
 }

ftplugin/quarto.lua

@@ -1,11 +1,9 @@
 
 
-local quarto_ok, quarto = pcall(require, 'quarto')
+local quarto = require('quarto')
-if quarto_ok then
+quarto.setup()
-  vim.keymap.set('n', '<leader>qp', quarto.quartoPreview, { silent = true, noremap = true, buffer = true })
+vim.keymap.set('n', '<leader>qp', quarto.quartoPreview, { silent = true, noremap = true })
-end
 
-if vim.bo.filetype == "r" then
 vim.keymap.set("n", "<Enter>", "<Plug>RDSendLine", { buffer = true })
 vim.keymap.set("v", "<Enter>", "<Plug>RSendSelection", { buffer = true })
 
@@ -14,15 +12,12 @@ if vim.bo.filetype == "r" then
 
 -- Pipe operator (;;)
 vim.keymap.set("i", ";;", "<Cmd>lua MiniTrailspace.trim()<CR><Plug>RInsertPipe<CR>", { buffer = true, noremap = true })
-end
 
-local runner_ok, runner = pcall(require, "quarto.runner")
+local runner = require("quarto.runner")
-if runner_ok then
+vim.keymap.set("n", "<localleader>a", runner.run_cell,  { desc = "run cell", silent = true })
-  vim.keymap.set("n", "<localleader>a", runner.run_cell,  { desc = "run cell", silent = true, buffer = true })
+vim.keymap.set("n", "<localleader>A", runner.run_all,   { desc = "run all cells", silent = true })
-  vim.keymap.set("n", "<localleader>A", runner.run_all,   { desc = "run all cells", silent = true, buffer = true })
 vim.keymap.set("n", "<localleader>RA", function()
   runner.run_all(true)
-  end, { desc = "run all cells of all languages", silent = true, buffer = true })
+end, { desc = "run all cells of all languages", silent = true })
-end
 
 

modules/module/settings/cat-packages.nix

@@ -43,7 +43,6 @@ in
       python313Packages.pylatexenc
       quartoPkg
       zk
-      marksman
     ]);
 
     nix = maybe "nix" (with pkgs; [
@@ -100,12 +99,13 @@ in
       quartoPkg
       pkgs.air-formatter
       pkgs.yaml-language-server
+      pkgs.rnvimserver
     ];
 
     # cats without packages get empty lists
     general = [ ];
     gitPlugins = [ ];
-    treesitterParsers = [ ];
+    treesitterParsers = [ pkgs.tree-sitter ];
     utils = [ ];
   };
 }

modules/module/settings/core.nix

@@ -14,6 +14,10 @@
   # Enable RC wrapping (allows neovim to find the config)
   config.settings.wrapRc = lib.mkDefault true;
 
+  # Lua packages available to neovim (for :lua require())
+  config.settings.nvim_lua_env = lp:
+    lib.optionals (config.cats.general or false) [ lp.tiktoken_core ];
+
   # Binary name for the wrapper
   config.binName = lib.mkDefault "vv";
 

modules/module/settings/env.nix

@@ -11,9 +11,10 @@
       UV_PYTHON_DOWNLOADS = "never";
       UV_PYTHON = pkgs.python.interpreter;
     })
-    # R.nvim v1.x owns its cache and temporary directories and exports
+    (lib.mkIf (config.cats.r or false) {
-    # RNVIM_COMPLDIR/RNVIM_TMPDIR during setup. Do not inject literal `$PWD`
+      RNVIM_COMPLDIR = "$PWD/.r-compl";
-    # values into the wrapper environment.
+      TMPDIR = "$PWD/.r-tmp";
+    })
   ];
 
   # Environment variables with defaults (can be overridden by user)

modules/module/settings/hosts.nix

@@ -22,6 +22,16 @@ in
         nvim-host.flags."--neovim-bin" = "${builtins.placeholder "out"}/bin/${config.binName}";
       };
 
+      m = {
+        nvim-host.enable = false;
+        nvim-host.package = "${pkgs.uv}/bin/uv";
+        nvim-host.argv0 = "uv";
+        nvim-host.addFlag = [
+          "run"
+          "marimo"
+          "edit"
+        ];
+      };
     }
     (lib.mkIf (config.cats.julia or false) {
       jl = {

modules/module/specs/plugins.nix

@@ -4,7 +4,6 @@
   lib,
   ...
 }: {
-
   config.specs.gitPlugins = lib.mkIf (config.cats.gitPlugins or false) {
     data = [];
   };
@@ -111,17 +110,13 @@
       nvim-lspconfig
       nvim-treesitter-context
       nvim-treesitter-textobjects
-      {
-        data = pkgs.vimPlugins.nvim-treesitter;
-        pname = "nvim-treesitter";
-      }
       {
         data = pkgs.codecompanion-nvim.overrideAttrs (old: {
           doCheck = false;
         });
         pname = "codecompanion";
       }
-    ] ++ builtins.attrValues pkgs.vimPlugins.nvim-treesitter.queries;
+    ];
   };
 
   config.specs.treesitterParsers = lib.mkIf (config.cats.treesitterParsers or false) {

plugin/00_options.lua

@@ -128,20 +128,27 @@ local diagnostic_opts = {
   -- Don't update diagnostics when typing
   update_in_insert = false,
 }
-later(function()
+later(function() vim.diagnostic.config(diagnostic_opts) end)
-  vim.diagnostic.config(diagnostic_opts)
+
+
+-- Custom autocommands ========================================================
+local augroup = vim.api.nvim_create_augroup('CustomSettings', {})
 
-  -- Relax diagnostics for markdown (many false positives)
 vim.api.nvim_create_autocmd('FileType', {
   pattern = { 'markdown' },
+  group = augroup,
   callback = function()
     vim.diagnostic.config({
-        signs = { severity = { min = 'WARN', max = 'ERROR' } },
+      signs = {
-        virtual_text = { severity = { min = 'HINT', max = 'ERROR' }, current_line = false },
+        severity = { min = 'WARN', max = 'ERROR' }
+      },
+      virtual_text = {
+        current_line = false,
+        severity = { min = 'HINT', max = 'ERROR' }
+      }
     })
-    end,
+  end
 })
-end)
 
 vim.api.nvim_create_autocmd("FileType", {
   desc = "remove formatoptions",
@@ -150,6 +157,17 @@ vim.api.nvim_create_autocmd("FileType", {
     vim.b.minitrailspace_disable = true        -- Don't highlight trailing space by default
   end,
 })
+
+vim.api.nvim_create_autocmd('FileType', {
+  group = augroup,
+  callback = function()
+    -- Don't auto-wrap comments and don't insert comment leader after hitting 'o'
+    -- If don't do this on `FileType`, this keeps reappearing due to being set in
+    -- filetype plugins.
+    vim.cmd('setlocal formatoptions-=r formatoptions-=o')
+  end,
+  desc = [[Ensure proper 'formatoptions']],
+})
 -- Neovide  ==============================================
 if vim.g.neovide then
   vim.g.neovide_cursor_vfx_mode = "pixiedust"
@@ -158,7 +176,7 @@ if vim.g.neovide then
   vim.g.neovide_cursor_short_animation_length = 0
   vim.g.neovide_font_hinting = 'none'
   vim.g.neovide_font_edging = 'subpixelantialias'
-  vim.o.guifont = 'JetBrainsMono Nerd Font:h14:#e-subpixelantialias:#h-none'
+  vim.o.guifont = 'JetBrainsMono Nerd Font,Symbols Nerd Font:h14:#e-subpixelantialias:#h-none'
   vim.g.neovide_floating_corner_radius = 0.35
   vim.keymap.set("n", "<leader>nf", "<cmd>NeovideFullscreen<CR>", { desc = "Toggle Neovide Fullscreen" })
 end

plugin/01_lib.lua

@@ -12,7 +12,7 @@ end
 
 Config.log = {}
 Config.log_buf_id = Config.log_buf_id or nil
-Config.start_hrtime = Config.start_hrtime or vim.uv.hrtime()
+Config.start_hrtime = Config.start_hrtime or vim.loop.hrtime()
 
 Config.log_print = function()
   if Config.log_buf_id == nil or not vim.api.nvim_buf_is_valid(Config.log_buf_id) then
@@ -24,7 +24,7 @@ end
 
 Config.log_clear = function()
   Config.log = {}
-  Config.start_hrtime = vim.uv.hrtime()
+  Config.start_hrtime = vim.loop.hrtime()
   vim.cmd('echo "Cleared log"')
 end
 

plugin/10_keymap.lua

@@ -66,28 +66,21 @@ nmap_leader('<Tab>', '<Cmd>bnext<CR>', 'Next buffer')
 nmap_leader('<S-Tab>', '<Cmd>bprev<CR>', 'Prev buffer')
 
 -- a is for 'AI'
-nmap_leader("aa", "<cmd>CodeCompanion /agent<CR>", "Agent chat (@{agent} tools)")
 nmap_leader("ac", "<cmd>CodeCompanionChat Toggle<CR>", "Chat Toggle")
-nmap_leader("aC", function()
+-- nmap_leader("ae", "<cmd>CodeCompanion /explain<CR>", "Explain Code")
-  local chat = require("codecompanion").last_chat()
+-- nmap_leader("af", "<cmd>CodeCompanion /fix<CR>", "Fix Code")
-  if not chat then
-    return vim.notify("No CodeCompanion chat to compact", vim.log.levels.WARN)
-  end
-  require("codecompanion.interactions.chat.context_management.compaction").compact(chat, { min_token_savings = 0 })
-end, "Compact chat")
 nmap_leader("ag", "<cmd>CodeCompanion /commit<CR>", "Generate commit message")
 nmap_leader("ai", "<cmd>CodeCompanionActions<CR>", "Chat Action")
 nmap_leader("al", "<cmd>CodeCompanion /lsp<CR>", "Explain LSP Diagnostics")
 nmap_leader("an", "<cmd>CodeCompanionChat Add<CR>", "Chat New")
 nmap_leader("as", "<cmd>CodeCompanion /suggest<CR>", "Suggest Improvements")
-nmap_leader("aw", "<cmd>CodeCompanion /tdd<CR>", "Workflow: plan, implement, test")
+--nmap_leader("ax", "<cmd>CodeCompanion /fixer<CR>", "Code Fixer")
 nmap_leader("ax", "<cmd>CodeCompanion /fixer<CR>", "Code Fixer")
-xmap_leader("aa", "<cmd>CodeCompanion /agent<CR>", "Agent on selection")
 xmap_leader("ae", "<cmd>CodeCompanion /explain<CR>", "Explain Code")
 xmap_leader("af", "<cmd>CodeCompanion /fix<CR>", "Fix Code")
-xmap_leader("ap", "<cmd>CodeCompanion /expert<CR>", "Code Expert")
+--xmap_leader("ap", "<cmd>CodeCompanion /expert<CR>", "Code Fixer")
+xmap_leader("ap", "<cmd>CodeCompanion /expert<CR>", "Code Fixer")
 xmap_leader("as", "<cmd>CodeCompanion /suggest<CR>", "Suggest Improvements")
-nmap_leader("ak", "<cmd>CodeCompanionChat adapter=codex<CR>", "Chat with Codex")
 
 -- b is for 'buffer'
 nmap_leader('bb', '<Cmd>b#<CR>', 'Alternate')
@@ -130,7 +123,7 @@ nmap_leader('fm', '<Cmd>Pick marks<CR>', 'Marks')
 nmap_leader('fn', '<cmd>ZkNotes<CR>', "Notes")
 nmap_leader('fk', '<Cmd>Pick keymaps<CR>', 'Keymaps')
 nmap_leader('fR', '<Cmd>Pick resume<CR>', 'Resume')
-nmap_leader('fp', '<Cmd>Pick files<CR>', 'Files')
+nmap_leader('fp', '<Cmd>Pick projects<CR>', 'Projects')
 nmap_leader('fq', '<Cmd>Pick list scope="quickfix"<CR>', 'Quickfix')
 nmap_leader('fr', '<Cmd>Pick lsp scope="references"<CR>', 'References (LSP)')
 nmap_leader('flr', '<Cmd>Pick lsp scope="references"<CR>', 'References (LSP)')
@@ -171,7 +164,7 @@ vim.keymap.set({ 'n' }, 'grk', '<Cmd>lua vim.lsp.buf.hover()<CR>', { desc = 'Doc
 vim.keymap.set({ 'n' }, 'gre', '<Cmd>lua vim.diagnostic.open_float()<CR>', { desc = 'Diagnostics' })
 
 nmap_lsp("K", '<Cmd>lua vim.lsp.buf.hover()<CR>', "Documentation")
-local formatting_cmd = '<Cmd>lua require("conform").format({ lsp_format = "fallback" })<CR>'
+local formatting_cmd = '<Cmd>lua require("conform").format({ lsp_fallback = true })<CR>'
 nmap_leader('la', '<Cmd>lua vim.lsp.buf.code_action()<CR>', 'Actions')
 nmap_leader('le', '<Cmd>lua vim.diagnostic.open_float()<CR>', 'Diagnostics popup')
 nmap_leader('lf', formatting_cmd, 'Format')
@@ -196,9 +189,11 @@ nmap_leader('Lx', '<Cmd>lua Config.execute_lua_line()<CR>', 'Execute `lua` line'
 
 -- o is for 'other'
 local trailspace_toggle_command = '<Cmd>lua vim.b.minitrailspace_disable = not vim.b.minitrailspace_disable<CR>'
+nmap_leader('od', '<Cmd>Neogen<CR>', 'Document')
 nmap_leader('oh', '<Cmd>normal gxiagxila<CR>', 'Move arg left')
 nmap_leader('ol', '<Cmd>normal gxiagxina<CR>', 'Move arg right')
 nmap_leader('or', '<Cmd>lua MiniMisc.resize_window()<CR>', 'Resize to default width')
+nmap_leader('oS', '<Cmd>lua Config.insert_section()<CR>', 'Section insert')
 nmap_leader('ot', '<Cmd>lua MiniTrailspace.trim()<CR>', 'Trim trailspace')
 nmap_leader('oT', trailspace_toggle_command, 'Trailspace hl toggle')
 nmap_leader('oz', '<Cmd>lua MiniMisc.zoom()<CR>', 'Zoom toggle')

plugin/20_startup.lua

@@ -208,37 +208,112 @@ now_if_args(function()
     on_attach = nil, -- (fun(buf: integer): boolean) return false to disable attaching
   }
 
-  local ts_filetypes = {
+
-    "c", "cpp", "lua", "nix", "python", "r", "markdown", "query",
+  local ok_configs, configs = pcall(require, "nvim-treesitter.configs")
-    "vim", "vimdoc", "yaml", "json", "toml", "rust", "go",
+
-    "javascript", "typescript", "tsx", "html", "css", "sql",
+  if ok_configs and configs.setup then
-    "julia", "rnoweb", "latex", "gitcommit", "gitignore",
+    local opts = {
-    "git_config", "git_rebase", "diff", "dockerfile",
+      highlight = { enable = true },
-    "make", "xml", "zig", "regex", "csv", "bash",
+      indent = { enable = false },
-    "markdown_inline", "quarto", "rmd", "codecompanion",
+      textobjects = {
+        move = {
+          enable = true,
+          set_jumps = true,
+          goto_next_start = {
+            ["]a"] = "@parameter.inner", -- fixed typo
+            ["]f"] = "@function.outer",
+            ["]o"] = "@loop.*",
+            ["]s"] = { query = "@local.scope", desc = "Next scope" },
+            ["]z"] = { query = "@fold", desc = "Next fold" },
+          },
+          goto_next_end = {
+            ["]M"] = "@function.outer",
+            ["]["] = "@class.outer",
+          },
+          goto_previous_start = {
+            ["[a"] = "@parameter.inner",
+            ["[f"] = "@function.outer",
+            ["[o"] = "@loop.*",
+            ["[s"] = { query = "@local.scope", query_group = "locals", desc = "Prev. scope" },
+            ["[z"] = { query = "@fold", query_group = "folds", desc = "Prev. fold" },
+          },
+          goto_previous_end = {
+            ["[M"] = "@function.outer",
+            ["[]"] = "@class.outer",
+          },
+          goto_next = {
+            ["]e"] = "@conditional.outer",
+          },
+          goto_previous = {
+            ["[e"] = "@conditional.outer",
+          },
+        },
+        swap = {
+          enable = true,
+          swap_next = {
+            ["<leader>x"] = "@parameter.inner",
+          },
+          swap_previous = {
+            ["<leader>X"] = "@parameter.inner",
+          },
+        },
+        lsp_interop = {
+          enable = true,
+          border = "none",
+          floating_preview_opts = {},
+          peek_definition_code = {
+            ["<leader>lm"] = "@function.outer",
+            ["<leader>lM"] = "@class.outer",
+          },
+        },
+      },
     }
-  local function start_treesitter(buf, filetype)
+
-    local lang = vim.treesitter.language.get_lang(filetype) or filetype
+
-    if #vim.api.nvim_get_runtime_file("parser/" .. lang .. ".*", false) == 0 then
+    -- Manual parser check for non-Nix users
-      return
+    if not Config.isNixCats then
+      local installed_check = function(lang)
+        return #vim.api.nvim_get_runtime_file("parser/" .. lang .. ".*", false) == 0
       end
-    vim.treesitter.start(buf, lang)
+      local to_install = vim.tbl_filter(installed_check, opts.ensure_installed)
-    vim.bo[buf].indentexpr = "v:lua.require('nvim-treesitter').indentexpr()"
+      if #to_install > 0 then
+        require("nvim-treesitter").install(to_install)
+      end
+    end
+    -- Environment-specific Overrides
+    if not Config.isNixCats then
+      opts.auto_install = true
+      opts.ensure_installed = Config.treesitter_helpers.default_parsers
+    else
+      opts.auto_install = false
+      -- Nix handles installation, so ensure_installed is skipped/empty
+    end
+
+
+    configs.setup(opts)
+    return
   end
 
   vim.api.nvim_create_autocmd("FileType", {
-    pattern = ts_filetypes,
+    pattern = "*",
-    callback = function(ev)
+    callback = function(args)
-      start_treesitter(ev.buf, vim.bo[ev.buf].filetype)
+      -- Use explicit buffer + filetype to avoid any ambiguity
+      local ok = pcall(vim.treesitter.start, args.buf, args.match)
+      vim.bo.syntax = 'on'
+      vim.bo.indentexpr = "v:lua.require'nvim-treesitter'.indentexpr()"
+      vim.wo[0][0].foldexpr = 'v:lua.vim.treesitter.foldexpr()'
+      vim.wo[0][0].foldmethod = 'expr'
     end,
   })
 
-  -- FileType may have fired before this deferred setup ran.
+  -- Textobjects: require plugin and bail out quietly if missing
-  if vim.bo.filetype ~= "" then
+  local ok_nto, nto = pcall(require, "nvim-treesitter-textobjects")
-    start_treesitter(0, vim.bo.filetype)
+  if not ok_nto then
+    return
   end
 
-  require("nvim-treesitter-textobjects").setup({
+  vim.g.no_plugin_maps = true
+  nto.setup({
     move = {
       set_jumps = true,
     },
@@ -247,36 +322,70 @@ now_if_args(function()
   local move = require("nvim-treesitter-textobjects.move")
   local swap = require("nvim-treesitter-textobjects.swap")
 
-  vim.keymap.set("n", "]a", function() move.goto_next_start("@parameter.inner", "textobjects") end, { desc = "Next parameter" })
+  -- Map motion function names to actual functions
-  vim.keymap.set("n", "[a", function() move.goto_previous_start("@parameter.inner", "textobjects") end, { desc = "Prev parameter" })
+  local move_fns = {
-  vim.keymap.set("n", "]f", function() move.goto_next_start("@function.outer", "textobjects") end, { desc = "Next function" })
+    goto_next_start     = move.goto_next_start,
-  vim.keymap.set("n", "[f", function() move.goto_previous_start("@function.outer", "textobjects") end, { desc = "Prev function" })
+    goto_next_end       = move.goto_next_end,
-  vim.keymap.set("n", "]o", function() move.goto_next_start("@loop.*", "textobjects") end, { desc = "Next loop" })
+    goto_previous_start = move.goto_previous_start,
-  vim.keymap.set("n", "[o", function() move.goto_previous_start("@loop.*", "textobjects") end, { desc = "Prev loop" })
+    goto_previous_end   = move.goto_previous_end,
-  vim.keymap.set("n", "]s", function() move.goto_next_start("@local.scope", "textobjects") end, { desc = "Next scope" })
+    goto_next           = move.goto_next,
-  vim.keymap.set("n", "[s", function() move.goto_previous_start("@local.scope", "locals") end, { desc = "Prev scope" })
+    goto_previous       = move.goto_previous,
-  vim.keymap.set("n", "]z", function() move.goto_next_start("@fold", "folds") end, { desc = "Next fold" })
+  }
-  vim.keymap.set("n", "[z", function() move.goto_previous_start("@fold", "folds") end, { desc = "Prev fold" })
-  vim.keymap.set("n", "]M", function() move.goto_next_end("@function.outer", "textobjects") end, { desc = "Next function end" })
-  vim.keymap.set("n", "][", function() move.goto_next_end("@class.outer", "textobjects") end, { desc = "Next class end" })
-  vim.keymap.set("n", "[M", function() move.goto_previous_end("@function.outer", "textobjects") end, { desc = "Prev function end" })
-  vim.keymap.set("n", "[]", function() move.goto_previous_end("@class.outer", "textobjects") end, { desc = "Prev class end" })
-  vim.keymap.set("n", "]e", function() move.goto_next("@conditional.outer", "textobjects") end, { desc = "Next conditional" })
-  vim.keymap.set("n", "[e", function() move.goto_previous("@conditional.outer", "textobjects") end, { desc = "Prev conditional" })
 
-  vim.keymap.set("n", "<leader>x", function() swap.swap_next("@parameter.inner", "textobjects") end, { desc = "Swap parameter next" })
+  -- All motions defined in one place
-  vim.keymap.set("n", "<leader>X", function() swap.swap_previous("@parameter.inner", "textobjects") end, { desc = "Swap parameter prev" })
+  -- spec = { query_or_list, query_group, desc }
+  local move_maps = {
+    goto_next_start = {
+      ["]a"] = { "@parameter.inner", "textobjects", "Next parameter" },
+      ["]f"] = { "@function.outer", "textobjects", "Next function start" },
+      ["]o"] = { { "@loop.inner", "@loop.outer" }, "textobjects", "Next loop" },
+      ["]s"] = { "@local.scope", "locals", "Next scope" },
+      ["]z"] = { "@fold", "folds", "Next fold" },
+    },
+    goto_next_end = {
+      ["]M"] = { "@function.outer", "textobjects", "Next function end" },
+      ["]["] = { "@class.outer", "textobjects", "Next class end" },
+    },
+    goto_previous_start = {
+      ["[a"] = { "@parameter.inner", "textobjects", "Previous parameter" },
+      ["[f"] = { "@function.outer", "textobjects", "Previous function start" },
+      ["[o"] = { { "@loop.inner", "@loop.outer" }, "textobjects", "Previous loop" },
+      ["[s"] = { "@local.scope", "locals", "Previous scope" },
+      ["[z"] = { "@fold", "folds", "Previous fold" },
+    },
+    goto_previous_end = {
+      ["[M"] = { "@function.outer", "textobjects", "Previous function end" },
+      ["[]"] = { "@class.outer", "textobjects", "Previous class end" },
+    },
+    goto_next = {
+      ["]e"] = { "@conditional.outer", "textobjects", "Next conditional" },
+    },
+    goto_previous = {
+      ["[e"] = { "@conditional.outer", "textobjects", "Previous conditional" },
+    },
+  }
 
-  if not Config.isNixCats then
+  -- Generate motion keymaps
-    local installed_check = function(lang)
+  for fn_name, maps in pairs(move_maps) do
-      return #vim.api.nvim_get_runtime_file("parser/" .. lang .. ".*", false) == 0
+    local fn = move_fns[fn_name]
-    end
+    if fn then
-    local default_parsers = Config.treesitter_helpers.default_parsers
+      for lhs, spec in pairs(maps) do
-    local to_install = vim.tbl_filter(installed_check, default_parsers)
+        local query_or_list, group, desc = spec[1], spec[2], spec[3]
-    if #to_install > 0 then
+        vim.keymap.set({ "n", "x", "o" }, lhs, function()
-      require("nvim-treesitter").install(to_install)
+          fn(query_or_list, group)
+        end, { desc = desc })
       end
     end
+  end
+
+  -- Swap keymaps (unchanged, but minimal)
+  vim.keymap.set("n", "<leader>x", function()
+    swap.swap_next("@parameter.inner")
+  end, { desc = "Swap with next parameter" })
+
+  vim.keymap.set("n", "<leader>X", function()
+    swap.swap_previous("@parameter.inner")
+  end, { desc = "Swap with previous parameter" })
 end)
 
 -- zk

plugin/21_datascience.lua

@@ -5,18 +5,18 @@ local add = Config.add
 local nix = require('config.nix')
 
 if not Config.isNixCats then
-  local add = MiniDeps.add
+  local m_add = MiniDeps.add
 
   now(function()
-    add({ source = "R-nvim/R.nvim" })
+    m_add({ source = "R-nvim/R.nvim" })
   end)
 
   now_if_args(function()
-    add({ source = "jmbuhr/otter.nvim" })
+    m_add({ source = "jmbuhr/otter.nvim" })
   end)
 
   later(function()
-    add({ source = "jpalardy/vim-slime" })
+    m_add({ source = "jpalardy/vim-slime" })
   end)
 end
 
@@ -44,6 +44,12 @@ end)
 -- r
 now(function()
   if nix.get_cat("r", false) then
+    local cwd = vim.fn.getcwd(-1)
+    vim.env.RNVIM_COMPLDIR = cwd .. "/.r-compl"
+    vim.env.R_LIBS_USER = (vim.env.R_LIBS_USER or ""):gsub("%$PWD", cwd)
+    vim.env.TMPDIR = cwd .. "/.r-tmp"
+    vim.fn.mkdir(vim.env.RNVIM_COMPLDIR, "p")
+    vim.fn.mkdir(vim.env.TMPDIR, "p")
     vim.g.rout_follow_colorscheme = true
     require("r").setup({
       -- Create a table with the options to be passed to setup()
@@ -56,20 +62,6 @@ now(function()
       rconsole_height = 20,
       nvimpager = "split_h",
       pdfviewer = "",
-      -- Use R.nvim's built-in rnvimserver-backed language server. Do not
-      -- configure the external R languageserver through plugin/25_lsp.lua.
-      r_ls = {
-        completion = true,
-        hover = true,
-        signature = true,
-        definition = true,
-        references = true,
-        implementation = true,
-        document_symbol = true,
-        workspace_symbol = true,
-        document_highlight = true,
-        rename = true,
-      },
     })
   end
 end)
@@ -77,6 +69,8 @@ end)
 
 -- Quarto
 now(function()
+  vim.treesitter.language.register("markdown", { "quarto", "rmd" })
+
   if nix.get_cat({ "r", "markdown" }, false) then
     vim.api.nvim_create_autocmd("FileType", {
       pattern = { "quarto" },

plugin/22_languages.lua

@@ -4,10 +4,10 @@ local later = MiniDeps.later
 local nix = require('config.nix')
 
 if not Config.isNixCats then
-  local add = MiniDeps.add
+  local m_add = MiniDeps.add
   later(function()
-    add({ source = "Bilal2453/luvit-meta" })
+    m_add({ source = "Bilal2453/luvit-meta" })
-    add({ source = "folke/lazydev.nvim" })
+    m_add({ source = "folke/lazydev.nvim" })
   end)
 end
 

plugin/23_editor.lua

@@ -2,10 +2,10 @@ local later = MiniDeps.later
 local add = Config.add
 
 if not Config.isNixCats then
-  local add = MiniDeps.add
+  local m_add = MiniDeps.add
 
   later(function()
-    add("stevearc/conform.nvim")
+    m_add("stevearc/conform.nvim")
   end)
 end
 
@@ -23,6 +23,20 @@ later(function()
       rmd = { "injected" },
       quarto = { "injected" },
     },
+
+    default_format_opts = {
+      lsp_format = "fallback",
+    },
+
+    formatters = {
+      my_styler = {
+        command = "R",
+        -- A list of strings, or a function that returns a list of strings
+        -- Return a single string instead of a list to run the command in a shell
+        args = { "-s", "-e", "styler::style_file(commandArgs(TRUE)[1])", "--args", "$FILENAME" },
+        stdin = false,
+      },
+    },
   })
 end)
 

plugin/24_completion.lua

@@ -4,7 +4,7 @@ local now = MiniDeps.now
 local now_if_args = Config.now_if_args
 
 -- Constants
-local BLINK_VERSION = "v1.10.2"
+local BLINK_VERSION = "v1.4.1"
 
 -- Plugin sources configuration
 local PLUGIN_SOURCES = {
@@ -26,16 +26,26 @@ local PLUGIN_ADDS = {
 -- Helper functions
 local function create_system_prompt(role_description)
   return function(context)
-    local lang = context.filetype or "programmer"
+    return "I want you to act as a senior " .. context.filetype .. " developer. " .. role_description
-    return "I want you to act as a senior " .. lang .. " developer. " .. role_description
   end
 end
 
 local function get_code_block(context)
-  local text = require("codecompanion.helpers.code").get_code(context.start_line, context.end_line)
+  local text = require("codecompanion.helpers.actions").get_code(context.start_line, context.end_line)
   return "```" .. context.filetype .. "\n" .. text .. "\n```"
 end
 
+local function create_common_opts(mapping, short_name)
+  return {
+    mapping = mapping,
+    modes = { "v" },
+    short_name = short_name,
+    auto_submit = true,
+    stop_context_insertion = true,
+    user_prompt = true,
+  }
+end
+
 local function get_mini_icons_highlight(ctx)
   local _, hl, _ = require("mini.icons").get("lsp", ctx.kind)
   return hl
@@ -47,7 +57,7 @@ local function get_blink_fuzzy_setting()
   }
 
   if not Config.isNixCats then
-    setting.prebuilt_binaries = { force_version = BLINK_VERSION }
+    setting.prebuilt_binary = { force_version = BLINK_VERSION }
   end
 
   return setting
@@ -55,10 +65,10 @@ end
 
 -- Plugin loading
 if not Config.isNixCats then
-  local add = MiniDeps.add
+  local m_add = MiniDeps.add
 
   now_if_args(function()
-    add({
+    m_add({
       source = "saghen/blink.cmp",
       depends = { "rafamadriz/friendly-snippets" },
       checkout = BLINK_VERSION,
@@ -67,64 +77,29 @@ if not Config.isNixCats then
 
   later(function()
     for _, source in ipairs(PLUGIN_SOURCES) do
-      add({ source = source })
+      m_add({ source = source })
     end
   end)
 end
 
 local function get_codecompanion_config()
   return {
-    adapters = {
-      acp = {
-        -- Codex = heavy agent lane (ChatGPT Edu login via `codex login`; ~/.codex/auth.json).
-        -- Requires `codex-acp` on PATH (~/.nix-profile/bin). ACP-only slash commands in the
-        -- chat buffer: /resume (restore a past session, fresh chat only), /mode (switch agent
-        -- mode), /command, /acp_session_options (e.g. model per session); `\` triggers ACP
-        -- command completion (1-5s delay after chat open).
-        codex = function()
-          return require("codecompanion.adapters").extend("codex", {
-            defaults = {
-              auth_method = "chatgpt",
-            },
-          })
-        end,
-      },
-    },
     interactions = {
       chat = {
         adapter = {
           name = "copilot",
-          model = "claude-sonnet-5",
+          model = "gemini-3.1-pro-preview",
-        },
-        slash_commands = {
-          ["share"] = {
-            opts = {
-              token = os.getenv("GITHUB_GIST_TOKEN"),
-            },
-          },
         },
         opts = {
           completion_provider = "blink",
-          context_management = {
-            editing = {
-              trigger = 0.65,
-              keep_cycles = 3,
-              exclude_tools = { "memory" },
-            },
-            compaction = {
-              trigger = 0.85,
-              min_token_savings = 10000,
-            },
-          },
         },
       },
       inline = {
         adapter = {
           name = "copilot",
-          model = "gpt-5-mini",
+          model = "gemini-3.1-pro-preview",
+        }
       },
-      },
-      shared = {
       keymaps = {
         accept_change = {
           modes = { n = "ga" },
@@ -137,24 +112,6 @@ local function get_codecompanion_config()
         },
       },
     },
-      background = {
-        adapter = {
-          name = "copilot",
-          model = "gpt-5-mini",
-        },
-        chat = {
-          callbacks = {
-            ["on_ready"] = {
-              actions = { "interactions.background.builtin.chat_make_title" },
-              enabled = true,
-            },
-          },
-          opts = {
-            enabled = true,
-          },
-        },
-      },
-    },
     display = {
       chat = {
         show_settings = false,
@@ -164,38 +121,12 @@ local function get_codecompanion_config()
           height = 0.33,
         },
       },
-      diff = {
-        enabled = true,
-        threshold_for_chat = 6,
-      },
-    },
-    rules = {
-      default = {
-        description = "Collection of common files for all projects",
-        files = {
-          ".clinerules",
-          ".cursorrules",
-          ".rules",
-          ".github/copilot-instructions.md",
-          "AGENT.md",
-          "AGENTS.md",
-          { path = "CLAUDE.md", parser = "claude" },
-          { path = "CLAUDE.local.md", parser = "claude" },
-          { path = "~/.claude/CLAUDE.md", parser = "claude" },
-        },
-      },
-      opts = {
-        chat = {
-          autoload = "default",
-          enabled = true,
-        },
-      },
     },
     prompt_library = {
       ["expert"] = {
         interaction = "chat",
         description = "Get expert advice from an LLM",
-        opts = { alias = "expert" },
+        --opts = create_common_opts("<localleader>ae", "expert"),
         prompts = {
           {
             role = "system",
@@ -215,7 +146,7 @@ local function get_codecompanion_config()
       ["fixer"] = {
         interaction = "chat",
         description = "Fix code errors with expert guidance",
-        opts = { alias = "fixer" },
+        --opts = create_common_opts("<localleader>af", "afixer"),
         prompts = {
           {
             role = "system",
@@ -235,7 +166,7 @@ local function get_codecompanion_config()
       ["suggest"] = {
         interaction = "chat",
         description = "Suggest improvements to the buffer",
-        opts = { alias = "suggest" },
+        --opts = create_common_opts("<localleader>as", "suggest"),
         prompts = {
           {
             role = "system",
@@ -257,53 +188,7 @@ local function get_codecompanion_config()
           },
         },
       },
-      ["agent"] = {
+    }
-        interaction = "chat",
-        description = "Agentic coding with the @{agent} tool group (read/edit/grep/run)",
-        opts = { alias = "agent" },
-        prompts = {
-          {
-            role = "user",
-            content = function(context)
-              return "@{agent} Work on the following code:\n\n" .. get_code_block(context) .. "\n\n"
-            end,
-            opts = { contains_code = true },
-          },
-        },
-      },
-      ["tdd"] = {
-        interaction = "chat",
-        description = "Workflow: plan the buffer change, implement it, run the tests",
-        opts = { alias = "tdd", is_workflow = true },
-        prompts = {
-          {
-            {
-              role = "user",
-              content = function(context)
-                return "Let's work test-driven. First, study #buffer and the relevant parts of the codebase, then propose a concise implementation plan (no code yet).\n\nThe code under discussion:\n\n"
-                  .. get_code_block(context)
-                  .. "\n\nThe task: "
-              end,
-              opts = { contains_code = true },
-            },
-          },
-          {
-            {
-              role = "user",
-              content = "Implement the plan now, writing or updating tests alongside the code. @{agent}",
-              opts = { auto_submit = true },
-            },
-          },
-          {
-            {
-              role = "user",
-              content = "Run the project's test suite with @{run_command} and fix any failures until it passes.",
-              opts = { auto_submit = true },
-            },
-          },
-        },
-      },
-    },
   }
 end
 
@@ -359,13 +244,6 @@ later(function()
 end)
 
 
--- CodeCompanion habit notes (chat buffer unless stated):
---   /compact  compact history, keep summary        /fork    fork the conversation
---   /symbols  insert symbols for a file            /share   export chat to a GitHub gist
---   gm        toggle "btw" ephemeral message       gty      YOLO: approve all tool calls
---   gba/gbd   buffer sync add/drop                 gd       debug window (adapter/tools info)
---   Codex (ACP) lane: /resume (fresh chat only), /mode, /command, /acp_session_options,
---   `\` ACP command completion. Prompt library: /expert /fixer /suggest /agent /tdd (workflow).
 later(function()
   add("codecompanion.nvim")
 
@@ -438,10 +316,7 @@ now_if_args(function()
     },
     snippets = { preset = "mini_snippets" },
     sources = {
-      per_filetype = {
+      default = { "references", "lsp", "path", "snippets", "buffer", "omni", "copilot", "codecompanion" },
-        codecompanion = { "codecompanion" },
-      },
-      default = { "references", "lsp", "path", "snippets", "buffer", "omni", "copilot" },
       providers = {
         path = {
           score_offset = 50,
@@ -460,6 +335,10 @@ now_if_args(function()
           score_offset = 10,
           opts = { cmp_name = "cmdline" }
         },
+        cmp_r = {
+          name = "cmp_r",
+          module = "blink.compat.source",
+        },
         copilot = {
           name = "copilot",
           module = "blink-copilot",

plugin/25_lsp.lua

@@ -8,14 +8,24 @@ if not Config.isNixCats then
 end
 
 now_if_args(function()
-  -- R.nvim owns the R `r_ls` client and starts its bundled rnvimserver from
-  -- its own plugin directory. Keep R out of this generic server registry.
   local servers = {
+    clangd = {},
     basedpyright = {},
     ruff = {},
     marksman = {
       filetypes = { "markdown", "markdown_inline", "codecompanion" },
     },
+    r_ls = {
+      filetypes = { 'r', 'rmd', 'rmarkdown' },
+      settings = {
+        ['r_ls'] = {
+          lsp = {
+            rich_documentation = true,
+            enable = true,
+          },
+        },
+      }
+    },
     julials = {
       settings = {
         julia = {