Suggested Changes to GXWF AGENT.md

1. Update TS backend branch reference

Current text says:

The TypeScript backend is in /Users/jxc755/projects/worktrees/galaxy-tool-util/branch/report_models.

The active worktree is now gxwf-web (branch gxwf-client). Update to:

The TypeScript backend is in the galaxy-tool-util monorepo — the active worktree lives at /Users/jxc755/projects/worktrees/galaxy-tool-util/branch/gxwf-web.

2. Note the clean API policy: clean everything, no key lists

Add a note under the clean operation description:

The clean operation intentionally exposes no key-level policy knobs (no allow/deny/preserve/strip lists). Users always get “clean everything.” The Python clean.py has more machinery but the API and CLI surface should stay simple.

3. Clarify report-shell scope and Nunjucks relationship

Current text says report-shell components are “shared between the web UI and CLI HTML output (via Nunjucks templates).” This is aspirational — the CLI HTML output side doesn’t exist yet. Rewrite to:

Report display components live in packages/gxwf-report-shell/ and are used by the web UI (gxwf-ui). CLI HTML output is planned via Nunjucks templates that consume the same report model JSON shapes; these are not yet implemented.

4. Python gxwf-web now serves gxwf-ui

Add:

The Python FastAPI server (gxwf-web) serves the gxwf-ui Vue SPA in production mode. Both backends (Python and TypeScript) can serve the same built UI artifact from packages/gxwf-ui/dist/.

5. OpenAPI sync workflow note

Add after the openapi.json reference:

To sync the OpenAPI spec from Python to TS: run make docs-openapi in the Python gxwf-web repo, then make sync-openapi in the TS monorepo, then pnpm codegen in packages/gxwf-web to regenerate api-types.ts. Commit openapi.json and api-types.ts together.

6. Remove or demote Jinja/Nunjucks HTML mention

Current text says “hopefully HTML in the future” for CLI output. The report-shell Vue components are the HTML story for the web UI. Nunjucks CLI HTML output is a separate effort. Clarify that Markdown is the current CLI output format; HTML output is the web UI.

7. Update the “not yet done” list

The document should reflect that:

• D8 (Format2 export from Galaxy) is complete
• D5 (Round-trip) is complete — 120/120 IWC workflows pass
• D7 (IWC lint-on-merge) is next in line
• D9 (VS Code) foundation is done; remaining: tool registry, completions

8. Clarify TS gxwf CLI subcommand structure

Add:

The TS CLI (packages/cli) exposes a single gxwf command with subcommands rather than the gxwf-* prefix namespace used by the Python CLIs. Convergence target: TS gxwf should have subcommands covering validate, clean, roundtrip, lint, to-format2, to-native.