Make lightcone-cli agent-agnostic: remove Claude Code integration - #168

lc init no longer installs a .claude/ plugin bundle, writes a project
CLAUDE.md, or takes --permissions; the plugin discovery module, the
wheel force-include, and the skills/agent-workflow docs are removed.
The lc eval harness is kept.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016EL5bESx3CqfMNZNPA1KHJ

init now creates what's missing, repairs the managed .gitignore block
and --scratch override, and never overwrites user files; a directory
that already holds an astra.yaml is adopted instead of rejected.
--check reports drift without writing (exit 1 when not converged);
--json emits {converged, created, repaired, unchanged, warnings}.

The spec scaffold now calls astra's boilerplate helper directly:
astra init's callback refuses non-empty directories and overwrites
.gitignore, both wrong for convergence.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016EL5bESx3CqfMNZNPA1KHJ

An empty gitignored placeholder is invisible in git, so it carried no
hint after clone. The README says outputs land in
results/<universe>/<output_id>/ via lc run and must not be written by
hand; the gitignore block becomes results/* + !results/README.md so
the one file stays tracked while outputs remain ignored.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016EL5bESx3CqfMNZNPA1KHJ

The venv exists to run analysis code; `lc` lives outside it (uv tool
install), and a second copy inside shadowed it with whatever version
PyPI resolved — unpinned, so even released drivers got skew. The venv
now installs requirements.txt (which the old venv never did), and the
execution-stack pin moves from requirements.txt into its own
Containerfile layer, where the image — the one place that genuinely
needs lightcone-cli — still gets it.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016EL5bESx3CqfMNZNPA1KHJ

requirements.txt changes on every dependency edit; the lightcone-cli
layer is the heavy one (snakemake, dask, distributed, dask-gateway)
and its pin rarely changes. Ordering it first keeps it cached across
requirements edits.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016EL5bESx3CqfMNZNPA1KHJ

Nothing ever read the baked copy: recipes run against the live project
tree (bind-mounted -v $PWD -w $PWD locally, shared filesystem on a
hub). Meanwhile compute_image_tag hashes every COPY source, so the
copy made each code edit change the tag and force a rebuild. The image
is now a pure environment — the tag moves only when the Containerfile
or dependency files change.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016EL5bESx3CqfMNZNPA1KHJ

With the image now a pure environment, directory COPY sources
(COPY . ., COPY src/) would only bake in a copy nothing executes —
recipes run against the live project tree — while forcing a full tree
hash on every tag computation and a rebuild on every code edit. They
now raise ContainerBuildError with guidance. Removes _COPY_DIR_EXCLUDE,
_hash_dir_into, and _copy_tree_filtered (~60 lines); file COPY sources
remain fully supported.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016EL5bESx3CqfMNZNPA1KHJ

Three moves cover the ten confirmed findings:

- One error boundary: CloudBuildError now subclasses
  ContainerBuildError, and the click group translates
  ContainerBuildError into a clean ClickException — lc run/build/
  status/cloudbuild all stop leaking tracebacks (findings 1-3).
- The converger repairs what lightcone wrote: _converge_file gains a
  repair(text)->str|None hook; legacy scaffold artifacts migrate
  forward (old Containerfile template -> current, lightcone-cli pin
  stripped from requirements.txt, blanket results/ gitignore rule
  narrowed so results/README.md stays tracked), and the warnings
  channel now carries what init sees but must not fix — hand-edited
  Containerfiles with directory COPYs (via the shared
  directory_copy_sources detector) and unparseable lightcone.yaml
  (findings 4, 5, 7, 8).
- Point fixes: eval loop prompt no longer invokes deleted skills;
  src/ scaffold claims removed from docstring and troubleshooting;
  the astra.yaml container: rewrite is a top-level-line regex with a
  warning fallback and a CI test pinning the result; the astra import
  fallback no longer swallows nested ImportErrors (findings 6, 9, 10).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016EL5bESx3CqfMNZNPA1KHJ

Projects from previous releases are not migrated: the verbatim
Containerfile upgrade, requirements pin-stripping, and blanket
results/ gitignore rewrite are gone along with their tests. What
remains is version-agnostic: the error boundary, the gitignore
append-once repair (adoption, not migration), the lightcone.yaml
parse guard, and the directory-COPY advisory warning.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_016EL5bESx3CqfMNZNPA1KHJ