Skill

vector-db-cleanup

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>

From vector-db

Install

Run in your terminal

npx claudepluginhub richfrem/agent-plugins-skills --plugin vector-db

Tool Access

This skill is limited to using the following tools:

BashReadWrite

Supporting Assets

View in Repository

assets/resources/architecture_sequence.mmd

assets/resources/deployment_model.mmd

assets/resources/rag_design_choices.md

assets/resources/stabilizers/README.md

assets/resources/stabilizers/vector_consistency_check.md

evals/evals.json

evals/results.tsv

requirements.in

requirements.txt

scripts/cleanup.py

scripts/init.py

scripts/query.py

scripts/vector_config.py

scripts/vector_consistency_check.py

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Stats

Parent Repo Stars1

Parent Repo Forks1

Last CommitApr 4, 2026

Actions

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vector-db-cleanup

From vector-db

Execution Protocol

1. Dry run -- show what will be removed

python3 ./scripts/cleanup.py \ --profile knowledge --dry-run

Report: "Found N orphaned chunks from X deleted files: [list of paths]"

2. Apply -- only after confirming with user

python3 ./scripts/cleanup.py \ --profile knowledge --apply

3. Verify store integrity (optional)

python3 ./scripts/vector_consistency_check.py \ --profile knowledge

4. Smoke test search still works

python3 ./scripts/query.py \ "test query" --profile knowledge --limit 3

Rules

Always dry-run first. Never apply without showing the user what will be deleted.

Never delete from .vector_data/ directly -- always use cleanup.py.

Never read .sqlite3 files with raw shell tools -- will corrupt context.

Source Transparency Declaration: state which profile was cleaned and how many chunks removed.

Dependencies

This skill requires Python 3.8+ and standard library only. No external packages needed.

To install this skill's dependencies:

pip-compile ./requirements.in
pip install -r ./requirements.txt

See ./requirements.txt for the dependency lockfile (currently empty — standard library only).

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. Always dry-run first.

When to Run

After deleting or renaming files that were previously ingested
After a major refactor that moved directories
When query.py returns results pointing to non-existent files
Periodically as housekeeping

Prerequisites

Verify server is running

If not already up, run the vector-db-launch skill first. For first-time setup (dependencies + profile config): run the vector-db-init skill.

curl -sf http://127.0.0.1:8110/api/v1/heartbeat