fix: skip generated git-tracked files during linting

[zeitlinger]

Summary

• skip lint targets that are marked as generated in git attributes
• keep Flint scoped to tracked files and preserve Flint-managed built-in excludes
• document that generated files should be marked in .gitattributes instead of Flint-only config when possible

Why

Generated files should not be part of ordinary lint runs, and storing that intent in git attributes lets GitHub and other tooling reuse the same metadata.

Root cause

Flint already limited full runs to git ls-files, but generic lint filtering did not consult git attributes for generated files, so tracked generated files could still be linted unless they were excluded in Flint-specific config.

Validation

• cargo test
• mise run lint:fix

[Copilot]

Pull request overview

Skips git-tracked files marked linguist-generated in .gitattributes during Flint's generic lint filtering, by invoking git check-attr from filter_names. Documentation in the README, CLI reference, and agent design notes is updated to recommend .gitattributes over Flint-only excludes for generated files.

Changes:

• Add generated_paths helper in src/files.rs that pipes tracked names through git check-attr --stdin -z linguist-generated and excludes any path with the attribute set, plus a new unit test that initializes a temp git repo with a .gitattributes file.
• Propagate Result from filter_names to callers (changed, all_files) so check-attr failures surface as errors.
• Update README, docs/cli.md, and .github/agents/knowledge/design.md to document the new behavior and recommend .gitattributes for shared generated-file metadata.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
src/files.rs	Adds generated_paths using git check-attr, threads it through filter_names, and adds a test for linguist-generated exclusion.
README.md	Clarifies tracked-files scope and adds an FAQ recommending .gitattributes for exclusions.
docs/cli.md	Updates the changed-file/baseline runs section to mention tracked-file scoping and linguist-generated skipping.
.github/agents/knowledge/design.md	Updates internal design notes for the two classes of excluded files.

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[martincostello]

LGTM except for the Copilot comment about deadlocks.

[zeitlinger]

close in favor of #305 - cla assistant not working