[P0-P2 tracker] Repository safety, test, documentation, CI, and packaging remediation

[realmarcin]

Goal

Track the repository-review remediation in dependency order. The linked issues contain implementation scope and acceptance criteria; this issue records priority and sequencing only.

P0: make routine development safe and green

These can run in parallel and should land first.

• [P0] Make just clean safe for tracked sources and documentation #663 — make just clean non-destructive
• [P0] Restore a green test suite by hardening dynamic imports and out-of-root subprocesses #664 — restore a green suite and deterministic subprocess/import tests

P1: publish accurate operational contracts

Start after P0 behavior is stable. #665 and #666 can run in parallel; #667 should establish the version and CI contract they document.

• [P1] Make provider CI triggers, Python support, and uv versions deterministic #667 — deterministic provider triggers, Python support, and uv versions
• [P1] Rebuild README quick start and examples from executable repository behavior #665 — rebuild README quick start and validated examples
• [P1] Rewrite CLAUDE.md as a current operational guide for agents #666 — rewrite CLAUDE.md as the current agent operational guide

P2: settle the distribution architecture

• [P2][Decision] Align packaging promises with checkout-dependent runtime paths #668 — decide between a checkout-dependent application and a supported installable package

Adjacent existing work

• The CI-trigger guard only follows gates invoked through just, not steps that run a tool directly #636 — broader limits of the CI-trigger guard
• Port CultureMech's KNOWN_BLOCKED provider check into deep_research_provider.py, and register the script for vendored-sync #658 — provider availability and vendored-sync drift

The new issues should cross-link rather than absorb those existing scopes.

Completion criteria

• All P0 and P1 issues are closed with their acceptance criteria met.
• The P2 decision is recorded and its implementation follow-ups are created.
• Full non-e2e tests, lint, and git diff --check are green.
• README and CLAUDE.md describe the same supported commands, paths, Python versions, and packaging model.