[BUG] deps list incorrectly reports embedded skills as orphaned for subdirectory dependencies

Describe the bug

When using a subdirectory dependency, apm deps list -g reports other embedded skills in the same repository as orphaned, while apm deps tree -g and apm prune correctly treat the dependency graph as clean.

To Reproduce

Given:

dependencies:
  apm:
    - git: yoshiko-pg/difit
      path: skills/difit

Run:

apm update -g --yes
apm deps list -g
apm prune

apm deps list -g reports unrelated embedded skills such as .codex/skills/release as orphaned, but apm prune reports:

No orphaned packages found. apm_modules/ is clean.

Expected behavior

apm deps list should not report embedded skills as orphaned when they are part of the same repository and are not independently resolved dependencies.

Environment

• OS: macOS
• APM Version: 0.30.0 (8c2e0d9)

Additional context

If this is confirmed to be a bug, I'd be happy to contribute a fix via PR.

Reproduce the issue with the provided dependencies configuration, then compare the implementation and output of apm deps list -g with apm deps tree -g and apm prune. Trace how each command identifies orphaned packages, focusing on subdirectory dependencies and embedded skills. Done means apm deps list -g no longer reports unrelated embedded skills as orphaned while the clean dependency behavior remains intact.