Update Catalog

Update Catalog

Regenerate the machine-readable Bactopia component index (catalog.json) and the AI-discovery surface (llms.txt) by invoking bactopia-catalog. Both files live at the repo root. The skill is a thin wrapper — all scanning, parsing, and rendering logic lives in bactopia-catalog in bactopia-py.

Steps

1. Tell the user you are checking for uncommitted local edits to catalog.json and llms.txt, then run:

   git -C /home/rpetit3/repos/bactopia/bactopia status --porcelain catalog.json llms.txt
   

   If either file is dirty, show the user the diff and confirm before overwriting. bactopia-catalog has no --force flag and silently clobbers existing output files, so this check is the user's only safety net against losing in-flight edits. If neither file is dirty, proceed directly to Step 2.

2. Run the wrapper to regenerate both files in one invocation:

   bash .agents/skills/update-catalog/scripts/run-bactopia-catalog.sh \
       --bactopia-path /home/rpetit3/repos/bactopia/bactopia \
       --output /home/rpetit3/repos/bactopia/bactopia/catalog.json \
       --pretty \
       --llms-output /home/rpetit3/repos/bactopia/bactopia/llms.txt
   

   • Always pass --pretty so the committed catalog.json stays diff-friendly.
   • --llms-output is what triggers llms.txt regeneration. Without it, only catalog.json is written. The user asked to update both — always pass it unless they explicitly say "catalog only".
   • The default llms.txt template is bundled inside bactopia-py at bactopia/templates/bactopia/llms.txt.j2. Do not pass --llms-template unless the user asks you to render from a non-default template path.

3. Summarize the result. Use the CLI's own summary line for counts (Found N modules, M subworkflows, K workflows) — don't parse the JSON yourself. Then show the user:

   • catalog.json path and the shape of the change (git diff --shortstat catalog.json)
   • llms.txt path and whether anything actually changed (git diff --shortstat llms.txt)
   • If a count changed (new or removed module/subworkflow/workflow), suggest /project-status for a full coverage read.

4. Do not stage or commit the updated files. Let the user review the diff first. Committing auto-generated files without human review is how stale or malformed content sneaks into main.

Notes

• Wrapper discovery order: PATH → bactopia-dev conda env → bactopia-py conda env → any bactopia-* env. Matches the shared pattern used by merge-schemas, project-status, update-module, and run-tests.
• --bactopia-path is always /home/rpetit3/repos/bactopia/bactopia — do not guess or prompt. This is a single-repo project.
• File locations: catalog.json and llms.txt both live at the repo root as of the catalog-location migration. Older references to data/catalog.json are stale.
• llms.txt is auto-generated — prose lives in the Jinja2 template at bactopia-py/bactopia/templates/bactopia/llms.txt.j2 (inside the bactopia-py package, not in this repo). If the user wants to change prose (headings, category highlights, key-patterns bullets), they should edit the template in bactopia-py, not llms.txt here. Running this skill without first editing the template will regenerate a byte-identical llms.txt.
• What's dynamic in the template: the module count line, the "Workflows (Tier 1)" list (looped over named workflows from the catalog), and the tool count. Everything else is hand-curated prose in the template.
• No --force guard in the CLI: bactopia-catalog silently overwrites whatever path --output / --llms-output point at. Step 1's dirty-check is the pragmatic substitute — don't skip it.
• Right follow-up after: /add-module, /add-subworkflow, /update-module (when schema or tool version changes affect catalog contents), or any manual edit to a module/subworkflow/workflow main.nf that changes GroovyDoc descriptions, contracts, or tags.

CLI Reference (bactopia-catalog)

Required:

• --bactopia-path PATH — directory where the Bactopia repository is stored

Catalog output:

• -o, --output PATH — where to write catalog.json (default: stdout, which is almost never what you want from a skill)
• --pretty — pretty-print JSON with 2-space indentation (always pass this so the committed file diffs cleanly)

llms.txt output:

• --llms-output PATH — where to write the rendered llms.txt. Omit to skip llms.txt rendering.
• --llms-template PATH — Jinja2 template path. Defaults to the bundled template inside bactopia-py (bactopia/templates/bactopia/llms.txt.j2). Rarely needed.

Other:

• --verbose, --version, --help

Sibling Skills

• /project-status — reads catalog.json via bactopia-status. A freshly regenerated catalog is immediately reflected in its output, so this is the natural read-after-write check.
• /merge-schemas — also reads catalog.json (for workflow path resolution). Run this after /update-catalog when a workflow's module set or schema has changed.
• /add-module, /add-subworkflow, /update-module — all three mutate the component graph. /update-catalog is the standard follow-up to keep catalog.json and llms.txt in sync.