Fixed doclinks to use git ls

[spomichter]

No description provided.

[greptile-apps]

Greptile Summary

Replaced manual .gitignore parsing and os.walk() traversal with git ls-files command for file discovery. This simplifies the codebase by removing ~60 lines of pattern-matching logic and delegates gitignore handling to git itself.

Key changes:

• Removed load_gitignore_patterns() and should_ignore() functions
• Added get_git_tracked_files() that calls git ls-files --cached --others --exclude-standard
• Simplified build_file_index() and build_doc_index() to iterate over git-tracked files instead of filesystem traversal

Benefits:

• More reliable: git's gitignore handling is authoritative and handles edge cases correctly
• Simpler: removes complex pattern matching logic (fnmatch, directory patterns, etc.)
• Consistent: ensures doclinks sees the exact same files git tracks

Confidence Score: 5/5

• This PR is safe to merge with minimal risk
• The refactoring replaces manual file filtering logic with git's native file tracking, which is more reliable and well-tested. The change is well-contained, maintains the same API contract, and simplifies the codebase significantly. Existing tests validate the behavior remains correct.
• No files require special attention

Important Files Changed

Filename	Overview
dimos/utils/docs/doclinks.py	Replaced manual .gitignore parsing with git ls-files for more reliable file tracking

Sequence Diagram

sequenceDiagram
    participant User
    participant doclinks
    participant Git
    participant FileSystem

    User->>doclinks: build_file_index(root)
    doclinks->>doclinks: get_git_tracked_files(root)
    doclinks->>Git: git ls-files --full-name --cached --others --exclude-standard
    Git-->>doclinks: list of tracked files
    doclinks->>doclinks: parse output into Path objects
    doclinks->>doclinks: build suffix index
    doclinks-->>User: file index (suffix → paths)

    User->>doclinks: build_doc_index(root)
    doclinks->>doclinks: get_git_tracked_files(root)
    doclinks->>Git: git ls-files --full-name --cached --others --exclude-standard
    Git-->>doclinks: list of tracked files
    doclinks->>doclinks: filter for .md files
    doclinks->>doclinks: build name index
    doclinks-->>User: doc index (name → paths)

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[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Exclude deleted paths from git file list

get_git_tracked_files relies on git ls-files --cached ... without checking if the paths still exist on disk. git ls-files keeps listing tracked files even after they are removed from the working tree until the deletion is staged, so deleting/renaming a tracked file and then running doclinks will still resolve links to that missing path instead of surfacing a "No file matching" error. The previous os.walk approach only indexed files present on disk, so this change can let broken links slip through whenever deletions are unstaged.

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