README.md

scripts/

Thin staging-root orchestrators. Heavy lifting stays in ../tools/ and ../cogant/ — the scripts here are glue that wires them together for end-to-end runs.

Script	Purpose
z_generate_manuscript_variables.py	Load METRICS.yaml, substitute {{VAR}} placeholders into manuscript/*.md, emit output/data/manuscript_variables.json plus a fully-populated output/manuscript/ tree (including config.yaml, references.bib, and preamble.md), and refresh output/figures/ from package-generated PNGs. Flags: --regenerate-metrics, --strict.
batch_dashboard.py	Cross-target dashboard generator — reads <output_root>/run_manifest.json plus each per-target bundle.json and writes <output_root>/dashboard/ (Markdown report, CSV, JSON, four Mermaid charts). Calls cogant.viz.batch_dashboard.BatchDashboardGenerator. Flags: --output-root, --dashboard-dir, --manifest, --quiet. See ../cogant/docs/reference/batch_dashboard.md.
../run_all.py	Staging-root sweep — run the configured COGANT chain over every target listed in run_all.json (or the embedded DEFAULT_CONFIG). The default output root is cogant/output; target directories are <output_root>/<id>/. The core order is export/render/viz/validate, followed by enabled post-validate steps such as roundtrip, API analysis/export, diagram/inspection artifacts, and batch dashboard generation. Local targets resolve via path; remote targets are cloned to _git_source/ from git_url. Entry point: ../run_all.sh (works from staging root or inner cogant/).

Quickstart

Generate the manuscript variables, regenerating metrics first:

uv run python scripts/z_generate_manuscript_variables.py --regenerate-metrics --strict

Sweep every configured codebase end-to-end:

./run_all.sh

The z_ prefix on z_generate_manuscript_variables.py keeps the script last when sorted alphabetically — it is intentionally the final stage in the manuscript pipeline. Paths are anchored on __file__, so the script runs identically from any cwd. See AGENTS.md for the rationale and full flag reference.