Report incomplete PR file inventories even without path matches

[roger-sato]

Summary

Path overlap reports can silently omit a known incomplete file inventory when none of its available paths match. A live read of PR #376 returned files: null; the existing collector correctly marked it truncated: true, but a fresh cache with matching head/base produced zero path hits, no warnings and no visible inventory gap.

Expose the sorted, unique PR numbers in coverage.pr_files.truncated_prs and warn independently of matching paths or --limit. Preserve truncated in combined term-and-path matches and their text rendering. complete_pagination continues to describe list paging; the documentation now explicitly separates that from completeness of each PR's file inventory. Fetching, cache contents, endpoint checks and mathematical sources are unchanged.

Test plan

Validation on macOS with CPython 3.12.14:

• 44 focused overlap/file/discussion tests pass, including five new actual subprocess CLI regressions covering no-hit fresh/offline caches, unavailable and short inventories, duplicate rows, result limits, combined matches, text output and a complete-empty control. The CLI fixtures disable executable lookup and preserve the cache bytes.
• The new regressions fail against the unchanged base helper. Replaying the PR Conditional κ=0.0011208649522582786: split centres with complete signed admission #376-derived cache after the fix exposes truncated_prs: [376] and the warning while retaining zero matches.
• git diff --check passes.

The full mathematical/selected replay and a full live file-index refresh were not run.

python3.12 -B -m unittest discover -s tests -p 'test_research_pr*.py' -v
python3.12 -B -m unittest discover -s tests -p 'test_research_overlap_*.py' -v
python3.12 -B -m unittest discover -s tests -p 'test_research_discussion_batch*.py' -v

Base: 20ecf2891d80b5acf18d980b2164fb44ea7faa90, priority revision 6. Scope refines verifier engineering to a concrete coordination-tool coverage failure. Targeted all-state PR searches, the current #1166 handoffs, and complete #1200 comments/replies found no same-scope follow-up; this is bounded metadata coverage, not a novelty guarantee.

Credit Douglas Colkitt's overlap/cache helper, Aaron Wang/navinor's #1623 path index, ywz65's #2517 continuation paging, Arham Tahir's #3104 head binding and Tekalign's #3141 base binding. Prepared with substantial OpenAI Codex assistance. No kappa or selected-frontier change.