fix: baseline lint coverage changes

.github/agents/knowledge/architecture.md

@@ -36,3 +36,24 @@ Template scopes:
 - `Files` — invoked once with all matched files (`{FILES}`)
 - `Project` — invoked once with no file args; skipped
   entirely if no matching files changed
+
+## Baseline Expansion
+
+Normal changed-file runs keep each check scoped to changed files. Before
+execution, `src/main.rs` also computes a set of checks that need a full file
+list to establish a new baseline.
+
+A check is expanded to all matching files when:
+
+- it was not active at the merge base, meaning its tool was newly added to
+  `mise.toml`
+- its resolved tool version changed in `mise.toml`
+- its registered `.linter_config(...)` file changed under `FLINT_CONFIG_DIR`
+- `flint.toml` changed under `[settings]`
+- `flint.toml` changed the check-specific section for a special check
+
+This is per-check. Unaffected checks still receive the normal changed-file list.
+Explicit `--full` bypasses this selection because every check is already using
+the all-files list. Config-change triggers use the raw git change list before
+`settings.exclude` is applied, so excluded config paths still expand the affected
+check.

default.json

@@ -38,6 +38,8 @@
     {
       "matchPackageNames": [
         "actionlint",
+        "biome",
+        "cargo:yaml-lint",
         "cargo:xmloxide",
         "editorconfig-checker",
         "github:google/google-java-format",
@@ -46,12 +48,10 @@
         "golangci-lint",
         "hadolint",
         "lychee",
-        "npm:@biomejs/biome",
-        "npm:markdownlint-cli2",
-        "npm:prettier",
         "npm:renovate",
         "pipx:codespell",
         "pipx:ruff",
+        "rumdl",
         "shellcheck",
         "shfmt"
       ],

docs/cli.md

@@ -35,6 +35,31 @@ Every flag has an env var equivalent: `FLINT_FIX`, `FLINT_FULL`, `FLINT_FAST_ONL
 | Pre-push hook (CC / agentic) | `flint run --fix --fast-only`          | Fixes what it can silently, surfaces only what needs human review |
 | CI                           | `flint run`                            | Full output for humans reading CI logs                            |
 
+## Changed-file and baseline runs
+
+By default, `flint run` checks only files changed relative to the merge base.
+Use `--full` to check every matching file explicitly.
+
+Some changed-file runs intentionally expand one or more affected checks to all
+matching files. This establishes a baseline when lint coverage changes, while
+leaving unrelated checks scoped to changed files.
+
+A check runs against all matching files when:
+
+- the check is newly active because its tool was added to `mise.toml`
+- the check's tool version changed in `mise.toml`
+- the check's flint-managed config file changed, such as `.shellcheckrc` or
+  `.yamllint.yml` in `FLINT_CONFIG_DIR`
+- `flint.toml` changed under `[settings]`
+- `flint.toml` changed the check-specific config for a special check, such as
+  `[checks.links]` or `[checks.renovate-deps]`
+
+`--full` is still the explicit whole-repo mode. The automatic baseline behavior
+only applies in changed-file mode, and only to checks whose lint coverage may
+have changed. Config-file triggers are detected from the raw git change list, so
+they still apply when the config path itself is excluded from ordinary lint file
+selection.
+
 **`--short` output** — failed checks partitioned by fixability, fixable ones
 expressed as the exact command to run:
 

src/files.rs

@@ -12,6 +12,8 @@ const BUILTIN_EXCLUDES: &[&str] = COMMITTED_PATHS;
 #[derive(Clone)]
 pub struct FileList {
     pub files: Vec<PathBuf>,
+    /// Changed paths from git before user excludes are applied.
+    pub changed_paths: Vec<String>,
     /// The merge base ref, used by project-scoped checks (e.g. golangci-lint).
     pub merge_base: Option<String>,
     /// True when the file list contains all project files (explicit --full or no merge base).
@@ -29,21 +31,26 @@ pub fn changed(
     let exclude = build_exclude_set(cfg);
 
     if full {
-        return all_files(project_root, &exclude);
+        return all(project_root, cfg);
     }
 
     let merge_base = resolve_merge_base(project_root, cfg, from_ref)?;
 
-    let files = if let Some(ref base) = merge_base {
+    let (files, changed_paths) = if let Some(ref base) = merge_base {
         let to = to_ref.unwrap_or("HEAD");
-        collect_changed_files(project_root, &exclude, base, to)?
+        let names = collect_changed_names(project_root, base, to)?;
+        (
+            filter_names(project_root, &exclude, names.clone()),
+            names.into_iter().collect(),
+        )
     } else {
         // No merge base (shallow clone etc.) — fall back to all files.
-        return all_files(project_root, &exclude);
+        return all(project_root, cfg);
     };
 
     Ok(FileList {
         files,
+        changed_paths,
         merge_base,
         full: false,
     })
@@ -88,12 +95,11 @@ fn resolve_merge_base(
     Ok(None)
 }
 
-fn collect_changed_files(
+fn collect_changed_names(
     project_root: &Path,
-    exclude: &GlobSet,
     base: &str,
     to: &str,
-) -> Result<Vec<PathBuf>> {
+) -> Result<std::collections::BTreeSet<String>> {
     let range = format!("{base}...{to}");
     let mut names: std::collections::BTreeSet<String> = Default::default();
 
@@ -110,7 +116,12 @@ fn collect_changed_files(
         names.insert(line);
     }
 
-    Ok(filter_names(project_root, exclude, names))
+    Ok(names)
+}
+
+pub fn all(project_root: &Path, cfg: &Config) -> Result<FileList> {
+    let exclude = build_exclude_set(cfg);
+    all_files(project_root, &exclude)
 }
 
 fn all_files(project_root: &Path, exclude: &GlobSet) -> Result<FileList> {
@@ -132,6 +143,7 @@ fn all_files(project_root: &Path, exclude: &GlobSet) -> Result<FileList> {
 
     Ok(FileList {
         files: filter_names(project_root, exclude, names),
+        changed_paths: vec![],
         merge_base: None,
         full: true,
     })

src/linters/renovate_deps.rs

@@ -520,6 +520,7 @@ mod tests {
     fn file_list(paths: &[&str], full: bool) -> FileList {
         FileList {
             files: paths.iter().map(PathBuf::from).collect(),
+            changed_paths: paths.iter().map(|path| path.to_string()).collect(),
             merge_base: Some("base".to_string()),
             full,
         }