fix(analysis): honor persisted submodule flags in health and dead-code

[RaghavChamadiya]

Problem

A repo initialized with --include-submodules persists the flag in .repowise/state.json, and the incremental update path reads it back (#381). The standalone analysis commands didn't: repowise health and repowise dead-code rebuilt the graph with a flagless FileTraverser/GraphBuilder, so on a submodule-indexed repo they analyzed a different (smaller) file set than was indexed — submodule files silently vanished from health metrics and dead-code reachability.

Fix

Read include_submodules / include_nested_repos from state.json the same way update_cmd does (missing key = legacy = False) and thread them into both constructions in health_cmd.py and dead_code_cmd.py. Both commands are read-only, so there's no persisted divergence to migrate.

Also drops a pre-existing unused resolve_repo_path import from the touched import block in dead_code_cmd.py.

Tests

tests/unit/cli/test_analysis_cmds_include_submodules.py — CliRunner-based, positive + negative for both commands against a repo with an initialized submodule (mirrors test_update_include_submodules.py).

• tests/unit/cli: 453 passed
• full tests/unit: 3783 passed, 2 xfailed
• ruff check clean on changed files

[repowise-bot]

✅ Health: 7.0 (unchanged)
_{1 file moved · 2 hotspots · 5 hidden couplings · 1 with fix history}

⚠️ Change risk: moderate _{(riskier than 42% of this repo's commits · raw 8.2/10)}
This change's risk is driven by:

• large diff (many lines added)
• scattered, high-entropy change

🩹 Review priority _{(files here with the most recent bug-fix history — defects cluster, so review these first)}

• .../commands/dead_code_cmd.py — fixed once in the last ~6 months

File	Score	Δ	Why
.../commands/health_cmd.py	5.6 → 5.5	▼ -0.1	score drifted on re-parse — no PR-attributable biomarkers

🔥 Hotspots touched (2)

• .../commands/health_cmd.py — 4 commits/90d, 1 dependents · primary owner: Raghav Chamadiya (98%)
• .../commands/dead_code_cmd.py — 7 commits/90d, 1 dependents · primary owner: Raghav Chamadiya (93%)

🔗 Hidden coupling (1 file)

• .../commands/dead_code_cmd.py co-changes with these files (not in this PR):
  • .../cli/helpers.py (3× — 🟢 routine)
  • .../commands/update_cmd.py (3× — 🟢 routine)
  • .../commands/doctor_cmd.py (2× — 🟢 routine)
  • .../server/app.py (2× — 🟢 routine)
  • README.md (2× — 🟢 routine)

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📊 Full report · ⭐ Star Repowise · 📥 Install bot · Last updated 2026-06-05 11:32 UTC
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