/codedna:check

Perform a CodeDNA compliance check on the current project. Do the following:

1. Find all source files in the project (.py, .php, .blade.php, .ts, .tsx, .js, .go, .java, .kt, .rb, .rs, .cs) — exclude vendor/, node_modules/, venv/, .venv/, .git/, __pycache__/, dist/, build/, migrations/.

2. Check each file for a CodeDNA module annotation:

   • Python: first token must be a string literal (module docstring) containing exports:, used_by:, and rules: fields.
   • Other languages: first comment block must contain exports:, used_by:, rules: fields.

3. Check for stale used_by: references: for every used_by: entry in every annotated file, verify the referenced file exists. Flag any references to files that no longer exist.

4. Check for missing agent: field in annotated Python files.

5. Output a report in this format:

CodeDNA Coverage Report
=======================
Total files:        <N>
Annotated:          <N> (<pct>%)
Unannotated:        <N>
Stale used_by refs: <N>

Unannotated files:
  - path/to/file.py
  - path/to/file.ts

Stale used_by references:
  - utils/format.py → used_by references deleted_file.py (file not found)

If all files are annotated and no stale references exist, output:

CodeDNA: all <N> files annotated, no stale references. Coverage: 100%