refactor(pipeline): step 5 — build-plane passes

[zaebee]

Step 5 of the language-packs migration (spec docs/specs/2026-10-14-language-packs-design.md "Build plane", plan docs/plans/2026-10-14-language-packs-step5.md, part of #146). The post-write passes live in the pipeline; the resolver no longer touches storage. No graph changes.

What moved

from	to
src/cgis/pipeline.py	src/cgis/pipeline/__init__.py — module stays cgis.pipeline, so all 32 importers are unchanged (no re-export; ruling P1)
src/cgis/resolver/uplift.py	src/cgis/pipeline/uplift.py — 100% rename

refresh_dispatch was already the pipeline's; its pure half dispatch_edges(methods, inheritance) stays in the resolver (P2). The resolver-storage allowlist is empty (spec acceptance): no cgis.resolver module imports cgis.storage, TYPE_CHECKING included.

Identity

• graph_identity.py diff, main 261cee3 vs this branch: cgis src/ @715cd9a identical (2019 / 7858), owner-api @8de2245 identical (19115 / 96258), ui/ identical (286 / 497).
• The final reviewer ran old (261cee3) and new code on the same tree with --domains and dumped every node and edge column (domains, ontology_class, metadata, DOMAIN_DEPENDS_ON): identical. Wheel and sdist contain the new package.
• A new test pins the post-write order (dispatch, then uplift), mutation-checked.

Self-graph ontology (fixed after review)

docs/ontology/domains.yaml still described the old layout: on the documented self-ingest the cgis.pipeline FILE node lost its domain, and every uplift node was tagged Pipeline and SemanticEngine (a false SemanticEngine → Pipeline domain edge). Pipeline now matches the package and owns the post-write passes; SemanticEngine drops its uplift patterns. Against main the only change is uplift's tag (SemanticEngine → Pipeline) and the SemanticEngine → StorageLayer domain edge disappearing — which is now true. Pinned by tests/self_parsing/test_domains_ontology.py.

Measurements and one re-baseline

• pipeline drift 0.072 → 0.106, unresolved 0.402 → 0.398 (lock 0.25 / 0.43).
• resolution drift 0.180 → 0.179, unresolved 0.440 → 0.452: uplift moved unchanged (28 unresolved of 70 calls, 0.40) out of a domain at 0.44, leaving 108/239 with no unresolved edge added. The plan stopped there; by decision the hygiene baseline went 0.45 → 0.46, with the arithmetic in patterns.yaml (the reviewer recounted it exactly). Nothing else was loosened.

Left for a follow-up (ruling P3)

Language knowledge still in cgis.resolver's text — the Python __init__ root rule in strip_layout_prefixes, the JS-builtins root in classify_fqn's generic tail, _is_dunder in DISPATCHES, and the language-named project state threaded through IndexBuilder.build. Removing them changes behaviour, so it should be its own measured change.

Deferred minors

• The order test pins dispatch-before-uplift, not "after persist/record" — that half is guarded by test_cli::test_ingest_full_db_with_domains_runs_uplift.
• Autodoc-owned HOW_IT_WORKS.md / pipeline_flow.mermaid and the demo ui/public/graph.json still name the old paths; they regenerate.

Gate: format, lint, mypy strict, 3231 passed, docstring 99%.

🤖 Generated with Claude Code

[gemini-code-assist]

Code Review

This pull request implements Step 5 of the Language Packs plan, refactoring the cgis.pipeline module into a package (cgis/pipeline/) and moving the semantic uplift module (uplift.py) from cgis/resolver/ to cgis/pipeline/. This change successfully decouples the resolver from storage operations, emptying the resolver-storage forbidden-edges allowlist. The PR also updates relevant documentation, domain configurations, and tests, including a new test to verify the order of post-write passes and a test suite for domain ontology tagging. No review comments were provided for this pull request.

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
96.6% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud