fix(scanner): isolate optional-stage failures and disambiguate skip causes

[gadievron]

Three bugs in core/scanner.py, fixed together as they share the
optional-stage skip/error machinery.

Error-handling: the optional enhance, verify and dynamic-test stages ran
inside step_context but had no inner try/except, unlike app-context and
llm-reachability. step_context re-raises (core/step_report.py:57), so an
optional-stage error escaped scan_repository to cli.py's blanket except and
discarded the completed parse/analyze work. Each optional stage now warns and
continues on failure, matching the existing app-context pattern. Required
stages (parse, analyze, build-output) still propagate their errors.

Skip-cause conflation: skipped_steps recorded one bare string for distinct
causes (verify auto-skip vs opt-out both -> 'verify'; dynamic-test collapsed
several causes -> 'dynamic-test'). Fixed additively: a new
skipped_step_reasons dict on ScanResult (emitted as steps_skipped_reasons in
scan.report.json) records the disambiguated cause per skipped step. The bare
skipped_steps / steps_skipped strings are unchanged so existing telemetry
consumers keep working.

New tests/test_scanner.py (7 tests; LLM/Docker stages monkeypatched so the
orchestration runs offline). Full suite 183 passed, 63 skipped, 0 failed.
ruff clean.

Co-Authored-By: Claude Opus 4.7 (1M context) noreply@anthropic.com

Coordination

Touches a file also modified by in-flight PR #25/#27/#69 (region-disjoint; textual merge only).

[gadievron]

Closing as already resolved on current master. This fix's behavior shipped via the parser-fix-stack release (#133/#134); confirmed by independent reproduction — the original bug (reconstructed from its bug-pipeline investigation) no longer manifests on master, not merely by line-presence. Part of a full validated sweep of the open-PR corpus.