richfrem/vector-db-cleanup
plugins/vector-db/skills/vector-db-cleanup/SKILL.md
Removes stale and orphaned chunks from the ChromaDB vector store for files that have been deleted or renamed. Use after files are removed or moved to keep the vector index in sync with the filesystem. <example> user: "Clean up the vector store after I deleted some files" assistant: "I'll use vector-db-cleanup to remove orphaned chunks." </example> <example> user: "The vector database has chunks for files that no longer exist" assistant: "I'll run vector-db-cleanup to prune them." </example>
$ install --global
skillsauthnpx skillsauth add richfrem/agent-plugins-skills vector-db-cleanupInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
Security Scan Results
3 of 9 scanners reported clean
Some scanners were skipped, did not run, or reported a non-clean status. Review each row below.
3
Scanners Passed
9
Scanners in report
Clean
TrivyContainer and dependency vulnerability scanner
95%
Clean
SemgrepStatic code analysis for vulnerabilities
95%
Clean
mcp-scan (Snyk)Model Context Protocol security validation
95%
Skipped
Snyk (dep)Open source security scanning
50%
Skipped
Socket.devSupply chain security analysis
50%
Skipped
VirusTotalMulti-engine malware detection
50%
Skipped
CrowdStrikeAdvanced threat intelligence
50%
Skipped
OSV-ScannerOpen Source Vulnerability database check
50%
Skipped
OWASP Dep-Check
50%
Last scanned: May 1, 2026, 1:20 AM190.4s1 file scanned
SKILL.md
- name:
- vector-db-cleanup
- plugin:
- vector-db
- description:
- |
- user:
- The vector database has chunks for files that no longer exist
- assistant:
- I'll run vector-db-cleanup to prune them.
- allowed-tools:
- Bash, Read, Write
Dependencies
This skill requires the chromadb and langchain packages defined in the plugin root.
VDB Cleanup Agent
Role
You remove stale and orphaned chunks from the ChromaDB vector store. A chunk is stale when its source file no longer exists on disk. Running this after deletes/renames keeps the vector index accurate and prevents false search results.
This is a write (delete) operation.
When to Run
- After deleting or renaming files that were previously ingested.
- After a major refactor that moved directories.
- When
query.pyreturns results pointing to non-existent files. - Periodically as housekeeping to maintain index health.
Execution Mode
This skill defaults to In-Process mode for zero-latency direct disk access. No background server is required.
Execution Protocol
1. Identify Search Profile
Verify available profiles in .agent/learning/vector_profiles.json. The default profile is usually wiki.
2. Run Cleanup
Note: The --profile flag is mandatory to ensure the correct collection and disk paths are loaded.
python ./scripts/cleanup.py --profile wiki
3. Verify Store Integrity (Optional)
Run the consistency check to verify that remaining facts are still supported.
python ./scripts/vector_consistency_check.py --profile wiki --topic .agent/learning/
Rules
- Profile Sovereignty: Always pass
--profileto ensure the correct semantic space is pruned. - API Integrity: NEVER attempt to delete chunks from the database SQLite files directly. Always use
cleanup.py. - Transparency: State which profile was cleaned and how many chunks were removed.
Related Skills
richfrem/issue-worktree-agent
testing
VerifiedTrustedCommunity
Skill for creating and managing isolated git worktrees (`.worktrees/issue-NNN`) for issue execution branches. USE ONLY when setting up or cleaning up isolated git worktrees for specific issue execution. DO NOT USE for managing local task files (use `task-agent`) or escalating tasks to issues (use `github-issue-backlog-agent`).
4SKILL.mdUpdated Jul 29, 2026
richfrem/issue-pr-lifecycle-agent
data-ai
VerifiedTrustedCommunity
Skill for orchestrating the end-to-end GitHub issue lifecycle flow: Issue -> Worktree -> Implementation -> PR Creation -> Resolution Closure. USE ONLY when running or dry-running full lifecycle orchestration for resolving an issue with a PR. DO NOT USE for isolated worktree management only (use `issue-worktree-agent`) or logging issues (use `github-issue-agent`).
4SKILL.mdUpdated Jul 29, 2026
richfrem/github-issue-prioritizer
tools
VerifiedTrustedCommunity
Automatically ranks GitHub issues (P0-P3) based on friction tier, frequency, and blockages, synchronizing priority labels and GitHub Projects v2 custom fields.
4SKILL.mdUpdated Jul 29, 2026
richfrem/github-issue-backlog-agent
testing
VerifiedTrustedCommunity
Bridge skill for escalating ephemeral local task scratchpad items (`tasks/*.md`) into durable, taxonomy-validated, evidence-rich GitHub Issues. USE ONLY when promoting a single-session local task into durable repository backlog. DO NOT USE for managing local kanban boards (use `task-agent` instead) or directly querying/commenting on issues (use `github-issue-agent` instead).
4SKILL.mdUpdated Jul 29, 2026