feat(discovery): explain skipped files and support build-ignore exceptions

[sims1253]

ry check . --explain-files now lists included files and skipped paths on stderr. This explains cases such as dtplyr's ignored vignette while keeping JSON diagnostics valid on stdout.

include-build-ignored = ["vignettes/benchmark.R"] adds a persistent exception to .Rbuildignore for CLI discovery and editor indexing. It preserves explicit config excludes, fixture settings, hidden/generated directory rules, symlink handling, and discovery caps. A skipped directory represents its subtree; explanations are bounded by index.max-files.

Validation: a fresh workspace build, workspace tests, Clippy with warnings denied, and formatting pass. Tests cover ignored ancestors across nested packages, narrow exceptions, config-exclude precedence, report limits, invalid globs, and the CLI's JSON output. The existing LSP protocol and discovery tests pass through the same shared walker.

Closes #363.

[coderabbitai]

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📥 Commits

Reviewing files that changed from the base of the PR and between 92c822a and e26979c.

📒 Files selected for processing (9)

• CHANGELOG.md
• crates/ry-cli/src/check.rs
• crates/ry-cli/src/main.rs
• crates/ry-cli/tests/config_e2e.rs
• crates/ry-config/src/config.rs
• crates/ry-workspace/src/discovery.rs
• crates/ry-workspace/src/lib.rs
• docs/configuration.md
• docs/usage.md

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[pullfrog]

Important

One behavior regression to resolve before merge: the new ancestor scan makes ry check <build-ignored-dir> silently discover zero files where base checked the subtree (exit code flips 1 → 0). Details inline, plus one docs nit.

Reviewed changes

• ry check --explain-files: new clap flag; rescan prints ry: include/ry: skip (reason) lines plus an omitted-count note per search root on stderr, keeping stdout (including JSON) clean; watch-mode polls stay quiet.
• SkippedPaths report in shared discovery: every prune site (symlink, ry.toml exclude, .Rbuildignore, hidden/generated directory, package support directory, test fixture) records a reason; non-source files are filtered, entries are capped at index.max-files with an omitted counter, and sorted.
• include-build-ignored config key: globs validated at load (InvalidIncludePattern), anchored at the config root, matched with require_literal_separator; threaded through Config default/merge so CLI and LSP both honor it.
• .Rbuildignore matching reworked to an ancestor scan plus an inherited_buildignore flag: ignored directories are entered when include patterns exist, children inherit the ignored state across nested-package boundaries, and each file is checked against the includes; excludes, fixture rules, and hidden-directory rules still take precedence.
• Tests: three shared_tests pinning narrow includes, nested-package inheritance, and the bounded report, plus an e2e test pinning valid JSON on stdout and explanation content on stderr; docs/configuration.md and docs/usage.md updated; CHANGELOG ### Added entry citing #363.

Verified locally: cargo fmt --check, clippy with -D warnings, and cargo test for ry-workspace --lib (43), ry-config --lib (34), and ry-cli --test config_e2e (41) all pass, plus empirical CLI probes of the include/explain behavior against both this branch and reverted base sources.

  ^{｜ Fix all ➔ ｜ Fix 👍s ➔ ｜ View workflow run ｜ Using openai-compatible/glm-5.3 ｜ 𝕏}

[pullfrog]

✅ No new issues found — both threads from the prior review are addressed cleanly.

Reviewed changes

• Bounded the .Rbuildignore ancestor scan at the walk root (crates/ry-workspace/src/discovery.rs): ry check <ignored-dir> again checks the subtree instead of silently discovering nothing and exiting 0, while inherited_buildignore still carries ignore state below entered directories so nested-package semantics and narrow includes are unchanged.
• Added the e2e regression test explicitly_requested_build_ignored_directory_still_gets_checked, pinning a non-zero exit, an RY000 diagnostic on stdout as valid JSON, and the include explanation on stderr for an explicitly requested build-ignored directory — it fails on the pre-fix commit and passes here (verified both).
• Documented the directory-versus-subtree distinction for include-build-ignored in docs/configuration.md (vignettes/** for the whole subtree; vignettes alone matches only the directory).

Verified locally: cargo fmt --check, cargo clippy -p ry-workspace -p ry-cli -- -D warnings, cargo test -p ry-workspace --lib (43 passed), and cargo test -p ry-cli --test config_e2e (42 passed) all green.

  ^{｜ View workflow run ｜ Using openai-compatible/glm-5.3 ｜ 𝕏}