Cross-repo validation rejects any project that has a coverage shadow row (::missed) #1609

Version

codebase-memory-mcp 0.10.2

(measured on 0.10.2; cr_store_has_exact_project is unchanged on main and in v0.10.3 as of 2026-08-14)

Platform

Windows (x64)

Install channel

GitHub release archive / install.sh / install.ps1

Binary variant

standard

What happened, and what did you expect?

Cross-repo passes reject perfectly healthy, fully indexed projects — as both source and target — with:

cross-repo source or target project is missing, invalid, or not indexed

cr_store_has_exact_project (src/pipeline/pass_cross_repo.c:123-131) requires the target store's projects table to hold exactly one row for the project. But any project with at least one parse_partial file carries the designed shadow row <name>::missed — the miss-graph that check_index_coverage reads. src/mcp/mcp.c:2414 documents that shadow rows must be ignored by consumers; this code path doesn't.

I expected shadow rows to be filtered here exactly as list_projects already does. This looks like the same bug class as #1044/#1046 (fixed) — a consumer of the projects table that predates the miss-graph and never learned to skip shadows; this is a new site.

Impact measured on a real fleet: 14 of 22 .NET repositories rejected from cross-repo linking. The trigger is chronic for .NET, because stock Visual Studio-generated Dockerfiles produce a permanent parse_partial (#1610), so virtually every .NET repo carries a shadow row at all times. There is no workaround at the tool level: delete_project filters shadow names, and no config key disables the miss-graph — we resorted to deleting the rows with direct SQL, which the next reindex undoes.

Reproduction

1. Code being indexed — any dummy repo whose root Dockerfile is the stock .NET shape (this alone yields parse_partial, see Dockerfile grammar flags stock .NET Dockerfiles as parse_partial #1610):

   FROM mcr.microsoft.com/dotnet/aspnet:8.0 AS base
   COPY --from=publish /app/publish .
   ENTRYPOINT ["dotnet", "App.dll"]

2. Index it and confirm the shadow row exists:

   codebase-memory-mcp cli index_repository --repo-path /tmp/demo --mode full
   # store's projects table now holds "demo" AND "demo::missed"
   

3. Run any cross-repo pass with this project as source or target.

   Result: cross-repo source or target project is missing, invalid, or not indexed.
   Expected: shadow rows ignored (as list_projects does) and the pass runs.

Logs

cross-repo source or target project is missing, invalid, or not indexed

Confirmations

• I searched existing issues and this is not a duplicate.
• My reproduction uses shareable code (a dummy snippet or a public OSS repository), not proprietary code.