fix: align biome init and formatter ownership

.github/agents/knowledge/design.md

@@ -8,21 +8,15 @@
 2. **`editorconfig-checker` deference**: `editorconfig-checker`
    (binary: `ec`) runs on all files but skips file types owned
    by active line-length-enforcing formatters (`cargo-fmt`,
-   `ruff-format`, `biome-format`, `prettier`). Implemented
+   `ruff-format`, `biome-format`, `rumdl`, `yaml-lint`). Implemented
    via `.defer_to_formatters()` on the `editorconfig-checker`
    entry. This avoids its `max_line_length` check conflicting
    with formatter output.
 
-3. **markdownlint + prettier on `*.md`**: Both checkers are
-   active when their tools are installed. They cover
-   different concerns (markdownlint: structural rules;
-   prettier: formatting). To avoid MD013 (line length)
-   conflicting with prettier's line wrapping, consuming
-   repos must disable MD013 in `.markdownlint.json`:
-
-   ```json
-   { "MD013": false }
-   ```
+3. **Rust-native docs/config stack**: Markdown is owned by
+   `rumdl`, YAML by `yaml-lint`, and JS/TS/JSON by `biome`.
+   This keeps ownership boundaries explicit and avoids the
+   old markdownlint/prettier overlap on `*.md`.
 
 4. **Fix mode runs serially**: `runner.rs` runs checks in
    parallel in check mode, but serially in fix mode to
@@ -43,6 +37,6 @@
    `BUILTIN_EXCLUDES` slice of paths that are always removed
    from the file list before any linter sees it. Currently
    contains `.github/renovate-tracked-deps.json` (a
-   generated file that should never be linted by prettier,
+   generated file that should never be linted by `rumdl`,
    ec, etc.). Add entries here — not in user-facing `exclude`
    docs — when a file is managed by flint itself.

.github/agents/knowledge/linters.md

@@ -31,7 +31,8 @@ Available builder modifiers:
 | `.mise_tool(name)`           | Look up availability under a different mise key (e.g. `rust` for `cargo-fmt`) |
 | `.version_req(range)`        | Restrict to a semver range (e.g. `">=1.0.0"`)                                 |
 | `.excludes(names)`           | Skip files already owned by these active checks                               |
-| `.slow()`                    | Mark as slow — skipped by `--fast-only`                                       |
+| `.slow()`                    | Mark as comprehensive-only and skipped by `--fast-only`                       |
+| `.adaptive()`                | Mark as comprehensive-only and relevance-gated in `--fast-only`               |
 | `.linter_config(file, flag)` | Inject a config flag when `FLINT_CONFIG_DIR/<file>` exists (see below)        |
 
 ## Config File Injection (`.linter_config`)
@@ -43,11 +44,11 @@ If the file is absent the flag is silently omitted — native config discovery
 remains in effect.
 
 ```rust
-// Example: markdownlint accepts --config <path>
-Check::file("markdownlint", "markdownlint {FILE}", &["*.md"])
-    .fix("markdownlint --fix {FILE}")
-    .linter_config(".markdownlint.json", "--config"),
-// → markdownlint --config /repo/.github/config/.markdownlint.json <file>
+// Example: rumdl accepts --config <path>
+Check::file("rumdl", "rumdl check {FILE}", &["*.md"])
+    .fix("rumdl check --fix {FILE}")
+    .linter_config(".rumdl.toml", "--config"),
+// → rumdl --config /repo/.github/config/.rumdl.toml check <file>
 ```
 
 **When NOT to use it:**

.github/renovate-tracked-deps.json

@@ -22,7 +22,9 @@
   "mise.toml": {
     "mise": [
       "actionlint",
+      "biome",
       "cargo:xmloxide",
+      "cargo:yaml-lint",
       "dotnet",
       "editorconfig-checker",
       "github:google/google-java-format",
@@ -33,12 +35,10 @@
       "hadolint",
       "lychee",
       "node",
-      "npm:@biomejs/biome",
-      "npm:markdownlint-cli2",
-      "npm:prettier",
       "npm:renovate",
       "pipx:codespell",
       "pipx:ruff",
+      "rumdl",
       "rust",
       "shfmt"
     ]

.gitignore

@@ -1,3 +1,4 @@
 .idea
 .mise.super-linter-*.toml
 /target
+.cache/

README.md

@@ -60,8 +60,9 @@ Add the linting tools your project needs alongside the `flint` binary itself:
 shellcheck              = "v0.11.0"
 "github:mvdan/sh"       = "v3.13.1"  # activates shfmt
 actionlint              = "1.7.10"
-"npm:markdownlint-cli2" = "0.47.0"
-"npm:prettier"          = "3.5.0"
+rumdl                   = "0.1.78"
+"cargo:yaml-lint"       = "0.1.0"
+biome                   = "2.4.12"
 rust                    = "1.87.0"    # activates cargo-fmt + cargo-clippy
 go                      = "1.24.0"    # activates gofmt
 lychee                  = "0.18.0"    # activates links check
@@ -176,14 +177,14 @@ Click a name in the table below for details. See the
 | [`ktlint`](docs/linters.md#ktlint)                             | Lint and format Kotlin code                                         | yes |
 | [`license-header`](docs/linters.md#license-header)             | Check source files have the required license header                 | —   |
 | [`lychee`](docs/linters.md#lychee)                             | Check for broken links                                              | —   |
-| [`markdownlint-cli2`](docs/linters.md#markdownlint-cli2)       | Lint Markdown files for style and consistency                       | yes |
-| [`prettier`](docs/linters.md#prettier)                         | Format Markdown and YAML files                                      | yes |
 | [`renovate-deps`](docs/linters.md#renovate-deps)               | Verify Renovate dependency snapshot is up to date                   | yes |
 | [`ruff`](docs/linters.md#ruff)                                 | Lint Python code                                                    | yes |
 | [`ruff-format`](docs/linters.md#ruff-format)                   | Format Python code                                                  | yes |
+| [`rumdl`](docs/linters.md#rumdl)                               | Lint Markdown files for style and consistency                       | yes |
 | [`shellcheck`](docs/linters.md#shellcheck)                     | Lint shell scripts for common mistakes                              | —   |
 | [`shfmt`](docs/linters.md#shfmt)                               | Format shell scripts                                                | yes |
 | [`xmllint`](docs/linters.md#xmllint)                           | Validate XML files are well-formed                                  | —   |
+| [`yaml-lint`](docs/linters.md#yaml-lint)                       | Lint YAML files for style and consistency                           | yes |
 
 <!-- registry-table-end -->
 <!-- editorconfig-checker-enable -->

docs/cli.md

@@ -39,7 +39,7 @@ Every flag has an env var equivalent: `FLINT_FIX`, `FLINT_FULL`, `FLINT_FAST_ONL
 expressed as the exact command to run:
 
 ```text
-flint: 2 checks failed — flint run --fix prettier cargo-fmt | review: shellcheck
+flint: 2 checks failed — flint run --fix rumdl cargo-fmt | review: shellcheck
 ```
 
 **`--fix` output** — fixes what's fixable, then prints the full output of
@@ -61,7 +61,7 @@ Pass one or more linter names to run only those:
 
 ```bash
 flint run shellcheck shfmt        # run only shellcheck and shfmt
-flint run --fix prettier          # fix only prettier
+flint run --fix rumdl             # fix only Markdown issues
 ```
 
 ## `flint update`
@@ -71,7 +71,7 @@ tool keys with their modern equivalents, preserving the declared version. Run it
 `flint run` reports an obsolete key error:
 
 ```text
-flint: obsolete tool key in mise.toml: "npm:markdownlint-cli" (replaced by "npm:markdownlint-cli2")
+flint: obsolete tool key in mise.toml: "github:mvdan/sh" (replaced by "shfmt")
   Run `flint update` to apply the migration automatically.
 ```
 

docs/linters.md

@@ -7,9 +7,9 @@ Every supported check, its config file (when applicable), and its scope. The
 config injection for `biome` and `biome-format` is not yet implemented.
 
 <!-- editorconfig-checker-disable -->
+<!-- markdownlint-disable MD013 -->
 <!-- linter-details-start -->
 <!-- Generated. Run `UPDATE_README=1 cargo test readme_linter_table_in_sync` to regenerate. -->
-
 ## `actionlint`
 
 |             |                                                    |
@@ -176,28 +176,6 @@ config = ".github/config/lychee.toml"
 check_all_local = true
 ```
 
-## `markdownlint-cli2`
-
-|             |                                               |
-| ----------- | --------------------------------------------- |
-| Description | Lint Markdown files for style and consistency |
-| Fix         | yes                                           |
-| Binary      | `markdownlint-cli2`                           |
-| Scope       | [file](#scopes)                               |
-| Patterns    | `*.md`                                        |
-| Config      | `.markdownlint.jsonc`                         |
-
-## `prettier`
-
-|             |                                |
-| ----------- | ------------------------------ |
-| Description | Format Markdown and YAML files |
-| Fix         | yes                            |
-| Binary      | `prettier`                     |
-| Scope       | [files](#scopes)               |
-| Patterns    | `*.md *.yml *.yaml`            |
-| Config      | `.prettierrc`                  |
-
 ## `renovate-deps`
 
 |             |                                                                                                                            |
@@ -207,6 +185,7 @@ check_all_local = true
 | Binary      | `renovate`                                                                                                                 |
 | Scope       | [special](#scopes)                                                                                                         |
 | Patterns    | `renovate.json renovate.json5 .github/renovate.json .github/renovate.json5 .renovaterc .renovaterc.json .renovaterc.json5` |
+| Run policy  | adaptive — runs in `--fast-only` only when relevant                                                                        |
 
 Verifies `.github/renovate-tracked-deps.json` is up to date by running Renovate locally and comparing its output against the committed snapshot. Requires `renovate` in `[tools]`.
 
@@ -241,6 +220,17 @@ exclude_managers = ["github-actions", "github-runners"]
 | Patterns    | `*.py`             |
 | Config      | `ruff.toml`        |
 
+## `rumdl`
+
+|             |                                               |
+| ----------- | --------------------------------------------- |
+| Description | Lint Markdown files for style and consistency |
+| Fix         | yes                                           |
+| Binary      | `rumdl`                                       |
+| Scope       | [file](#scopes)                               |
+| Patterns    | `*.md`                                        |
+| Config      | `.rumdl.toml`                                 |
+
 ## `shellcheck`
 
 |             |                                        |
@@ -272,26 +262,47 @@ exclude_managers = ["github-actions", "github-runners"]
 | Scope       | [files](#scopes)                   |
 | Patterns    | `*.xml`                            |
 
+## `yaml-lint`
+
+|             |                                           |
+| ----------- | ----------------------------------------- |
+| Description | Lint YAML files for style and consistency |
+| Fix         | yes                                       |
+| Binary      | `yaml-lint`                               |
+| Scope       | [files](#scopes)                          |
+| Patterns    | `*.yml *.yaml`                            |
+| Config      | `.yamllint.yml`                           |
+
 <!-- linter-details-end -->
+<!-- markdownlint-enable MD013 -->
 <!-- editorconfig-checker-enable -->
 
 ## Scopes
 
 - `file` — invoked once per matched file
-- `files` — invoked once with all matched files as args; only changed files are passed
+- `files` — invoked once with all matched files as args; only changed files are
+  passed
 - `project` — invoked once with no file args; for checks with patterns set
-  (e.g. `cargo-clippy`), skipped entirely if no matching files changed, but runs on
-  the whole project when it does run. `golangci-lint` is the exception — it uses
+  (e.g. `cargo-clippy`), skipped entirely if no matching files changed, but
+  runs on the whole project when it does run. `golangci-lint` is the
+  exception — it uses
   `--new-from-rev` to scope analysis to changed code even within the project run.
 
-Checks tagged slow in the registry are skipped by `--fast-only`. Use
-`--fast-only` for local/pre-push feedback and the full set in CI. (No
-builtin is currently marked slow, but the mechanism is preserved.)
+Checks use one of three run policies:
+
+- `fast` — always runs, including in `--fast-only`
+- `slow` — skipped by `--fast-only`
+- `adaptive` — runs in `--fast-only` only when the changed files are relevant
+
+Use `--fast-only` for local/pre-push feedback and the full set in CI.
 
-**`editorconfig-checker` defers to formatters**: `editorconfig-checker` runs on all files, but
+**`editorconfig-checker` defers to formatters**: `editorconfig-checker` runs on
+all files, but
 automatically skips file types owned by an active line-length-enforcing
-formatter. When `cargo-fmt`, `ruff-format`, `biome-format`, or `prettier`
-are active, their file types are excluded from `editorconfig-checker` — those formatters
+formatter. When `cargo-fmt`, `ruff-format`, `biome-format`, `rumdl`, or
+`yaml-lint`
+are active, their file types are excluded from `editorconfig-checker` — those
+formatters
 already enforce line length and would conflict with `editorconfig-checker`'s
 `max_line_length` editorconfig check. If none of those formatters are
 installed, `editorconfig-checker` checks those files itself.

docs/why.md

@@ -72,4 +72,4 @@ use everywhere" promise of mise. Container startup also adds latency to every ru
 
 5. **Autofix where possible** — `--fix` checks first, fixes what's fixable,
    reports what needs review. Fix mode runs serially to avoid concurrent writes.
-   Pass specific linter names to limit which fixers run (`flint run --fix prettier shfmt`).
+   Pass specific linter names to limit which fixers run (`flint run --fix rumdl shfmt`).

mise.toml

@@ -2,16 +2,15 @@
 FLINT_CONFIG_DIR = ".github/config"
 
 [tools]
+biome = "2.4.12"
 lychee = "0.22.0"
-node = "24.15.0"
 "npm:renovate" = "43.129.0"
 "github:koalaman/shellcheck" = "v0.11.0"
 shfmt = "v3.13.1"
 actionlint = "1.7.10"
 editorconfig-checker = "v3.6.1"
-"npm:markdownlint-cli2" = "0.22.0"
-"npm:prettier" = "3.8.3"
-"npm:@biomejs/biome" = "2.4.12"
+"cargo:yaml-lint" = "0.1.0"
+"rumdl" = "0.1.78"
 "pipx:ruff" = "0.15.11"
 "pipx:codespell" = "2.4.2"
 rust = { version = "1.95.0", components = "clippy,rustfmt" }
@@ -24,6 +23,7 @@ dotnet = "10.0.201"
 "cargo:xmloxide" = "0.4.1"
 golangci-lint = "2.11.4"
 "github:google/google-java-format" = "1.35.0"
+node = "24.15.0"
 
 [tasks."setup:update-super-linter-versions"]
 description = "Generate super-linter version mapping from the super-linter repo"

src/files.rs

@@ -171,5 +171,24 @@ fn filter_names(
         .filter(|name| !BUILTIN_EXCLUDES.contains(&name.as_str()))
         .filter(|name| !exclude.is_match(name))
         .map(|name| project_root.join(name))
+        .filter(|path| path.exists())
         .collect()
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn filter_names_skips_deleted_worktree_paths() {
+        let tmp = tempfile::TempDir::new().unwrap();
+        std::fs::write(tmp.path().join("present.md"), "ok\n").unwrap();
+        let names = ["missing.md".to_string(), "present.md".to_string()]
+            .into_iter()
+            .collect();
+
+        let files = filter_names(tmp.path(), &GlobSetBuilder::new().build().unwrap(), names);
+
+        assert_eq!(files, vec![tmp.path().join("present.md")]);
+    }
+}