refactor(P4a): stop reconfiguring root logging at import in 20 modules

[LukasWodka]

Summary

Structural refactor — phase P4 (config injection), first slice. Twenty modules (every validator + database + file_transfer) called setup_logging(config) at import time — reconfiguring the root logger's handlers globally, 20× on every import. That's an import-time side effect a library shouldn't have. The entrypoints (cli/run.main and the template scripts) already call setup_logging() at startup, so the per-module calls were redundant.

This removes the import-time setup_logging(config) call + its now-unused import from all 20 modules. Each module keeps config = Config() and logger.setLevel(config.LOG_LEVEL) — the full config-by-construction + env-var-bridge removal are the next P4 slices (below). Logging is now configured once, at the app entrypoint.

Behaviour preservation

Root logging is still configured by the entrypoint; child loggers inherit. Diff is exactly the 20 files (just the 2-line removal each).

• Full unit suite: 1078 passed, 1 xfailed, coverage 96.9%.
• e2e (real MySQL): 23 passed, 1 xpassed — the test(e2e): characterization harness pinning clean-ingest behavior per modality #247 characterization goldens are unchanged.

What's next in P4

This was the safe, e2e-independent slice. The config-by-construction core follows:

• P4b — inject Config into the file validators (via the registry's build_validators) instead of the module-level global.
• P4c — file_transfer takes resolved paths as parameters; delete cli/run._set_legacy_env_vars (the os.environ bridge). The e2e-sensitive part — now gateable with the local harness (Docker confirmed working).

(Pre-existing flake8 noise in some touched files — unused List/Optional/pd etc. — is unrelated and left out of scope.)

🤖 Generated with Claude Code

[LukasWodka]

👋 Heads-up — Code review queue is at 11 / 8

Above the WIP limit. The team convention is to review existing PRs before opening new work.

Open PRs currently in Code review (oldest first):

• averaging-service#115 — Release: staging → main (averaging correctness sweep → production) · author: @aptracebloc · no reviewer assigned
• cli#78 — fix(dataset rm): delete staging files from a uid-65532 pod, not jobs-manager (Release v0.3.10 (ingestion hardening + path-traversal fix + single-label preflight) #259) · author: @LukasWodka · no reviewer assigned
• cli#79 — chore(schema): re-sync vendored ingest.v1.json from data-ingestors master · author: @LukasWodka · no reviewer assigned
• client-runtime#108 — fix(authz): match ingest table prefixes at a segment boundary (close cross-tenant straddle) · author: @LukasWodka · no reviewer assigned
• data-ingestors#270 — docs(releasing): correct ingestor rollout — floating tag + imagePullPolicy=Always, not INGESTOR_IMAGE_DIGEST rewrite · author: @saadqbal · no reviewer assigned
• design-system#47 — feat(table): Table compound organism (Figma 959:6061 + 986:9822) · author: @waqaskhanroghani · no reviewer assigned
• frontend-app#523 — test(cypress): session + protected-route + error-state + endurance E2E coverage (and 2 bug fixes) · author: @waqaskhanroghani · no reviewer assigned
• frontend-app#526 — feat(observability): error boundaries that report to Application Insights · author: @waqaskhanroghani · no reviewer assigned
• frontend-app#527 — ci: add a type-check gate over production source · author: @waqaskhanroghani · no reviewer assigned
• tracebloc-py-package#218 — fix(upload): output-shape validation + hard-fail class-count check for text_classification · author: @shujaatTracebloc · reviewer: @aptracebloc

Pull from review before opening new work. (This is a nudge from the kanban WIP check, not a block.)