Link commands fail with 'KB not found' for newly registered KBs

[markramm]

Bug Description

The kb link and kb links bulk-create commands fail with Error: KB not found for a newly registered and indexed KB, even though kb search, kb get, kb list, and kb tags all work correctly for the same KB.

Steps to Reproduce

1. Create a new KB directory with kb.yaml and entries
2. Register it: kb kb add /path/to/kb -n my-kb -t network-investigation -d "description"
3. Index it: kb kb reindex -k my-kb → succeeds, shows entries added
4. Verify search works: kb search "test" -k my-kb → succeeds, returns results
5. Verify get works: kb get entry-id -k my-kb → succeeds
6. Try to create a link: kb link source-id target-id -k my-kb -r related_to → fails with "KB not found"
7. Try bulk links: kb links bulk-create file.yaml -k my-kb → same error
8. Also fails: kb kb validate my-kb → "KB not found"
9. Also fails: kb orient -k my-kb → "KB not found"

Expected Behavior

All commands should find the KB consistently once it's registered and indexed.

Actual Behavior

Search index commands (search, get, tags, list-entries, reindex) work fine.
Link commands, validate, and orient all fail with "KB not found".

This suggests the link subsystem uses a different registry/DB lookup path than the search subsystem.

Environment

• Pyrite version: latest (as of 2026-04-03)
• KB type: network-investigation
• Entries: 106
• Registration method: kb kb add followed by kb kb reindex

Workaround Attempted

Removed and re-added the KB — same result. The search index is correctly populated but the link/validate/orient subsystems can't find the KB.

Affected Commands

• kb link ❌
• kb links bulk-create ❌
• kb kb validate ❌
• kb orient ❌
• kb search ✅
• kb get ✅
• kb tags ✅
• kb list-entries ✅
• kb kb reindex ✅
• kb kb list ✅ (shows KB in registry)

Investigation Notes

The main Pyrite DB at ~/.pyrite/pyrite.db appears empty (.tables and .schema return nothing), while the search index is populated. The link system may be looking for entries in the main DB rather than the search index, and the main DB may not have been provisioned for this KB type.

[markramm]

Additional Finding

The issue is not just find_file. The PyriteConfig.get_kb() returns None for thiel-network when called through the CLI command path, even though:

1. The KB is registered in ~/.pyrite/config.yaml (I added it manually)
2. load_config() finds it correctly when called from Python directly
3. kb kb list shows it (uses a different code path)
4. kb search and kb get find it (use the index DB, not config)

The link/validate/orient commands go through KBService → config.get_kb() which returns None, even though the config file has the entry. There may be a config caching issue, or kb kb add updates one registry (the kbs/ directory or index DB) without updating the config.yaml that KBService reads.

The find_file fix addresses a different bug (entry lookup within a KB). This KB-level lookup failure is a separate issue in the config/registry dual-store architecture.