Problem

Manual additions to code-trace-index.json (marking files as traced via the traced_files field) are silently overwritten when the solve pipeline regenerates the index. The C→R residual never decreases because user-acknowledged traces are lost.

Reproduction

1. C→R scanner reports bin/aggregate-requirements.cjs as untraced (residual=2)
2. User adds it to code-trace-index.json:

   {
     "traced_files": {
       "bin/aggregate-requirements.cjs": {
         "traced_to": "TOOL-INTERNAL",
         "reason": "nForma toolchain"
       }
     }
   }

3. Next solve run or hook regenerates the file, resetting traced_files to {}
4. C→R residual stays at 2

Expected Behavior

• traced_files entries added by users should be preserved across regeneration
• The regeneration logic should merge new data with existing user entries, not overwrite
• Alternatively, provide a separate acknowledged-traces.json file that is user-owned and never auto-generated

Impact

Users cannot reduce C→R residual. The "trace a module to a requirement" workflow is broken because the persistence layer doesn't respect manual entries.