ci: post-Phase-2-docs-overhaul cleanup of stale guards + missing config doc

CI run on the ecb8896 push surfaced two real failures rooted in the
2026-05-04 docs overhaul:

  1. G-3 env-docs-drift caught two phantom CERTCTL_* env vars I'd
     introduced in the Phase 4 follow-on connector pages
     (CERTCTL_CA_CERT_PATH_NEW in adcs.md was a placeholder I made
     up; CERTCTL_EJBCA_POLL_MAX_WAIT_SECONDS in ejbca.md does not
     exist in source). Both removed.

  2. QA-doc Part-count drift guard tried to grep
     docs/qa-test-guide.md and docs/testing-guide.md, both of which
     were renamed/deleted in Phase 2/Phase 5. The Part-count drift
     class died with testing-guide.md (Phase 5 prune dispersed its
     content); the seed-count drift class is still live but pointed
     at the wrong path.

Fixes:

- Removed the QA-doc Part-count drift guard from ci.yml (premise
  dead) plus its standalone scripts/qa-doc-part-count.sh peer.
- Retargeted the QA-doc seed-count drift guard from
  docs/qa-test-guide.md → docs/contributor/qa-test-suite.md (the
  Phase 2 target). Updated both ci.yml inline copy and
  scripts/qa-doc-seed-count.sh.
- Updated Makefile qa-stats: target to drop the testing-guide.md
  Parts metric (file is gone).
- Updated Makefile verify-docs: target to drop the part-count step.

G-3 was also failing in the second direction (env vars defined in
config.go but never documented anywhere). 16 vars surfaced —
features.md (deleted Phase 6) and testing-guide.md (deleted Phase 5)
had been their canonical home. Created
docs/reference/configuration.md as the new home: a compact
operator-facing env-var reference covering scheduler intervals, job
lifecycle, rate limiting, audit, deploy verify, database,
agent-side, and SCEP profile binding. Added to docs/README.md
Reference table.

Doc-side updates to qa-test-suite.md to reframe its references to
the deleted testing-guide.md (it's now self-contained: the
Part-by-Part Coverage Map IS the canonical Part inventory).

Cosmetic comment-only updates in ci.yml + scripts/ci-guards/*.sh +
scripts/dev-setup.sh to point at the new audience-organized doc
paths (docs/operator/security.md, docs/operator/tls.md,
docs/reference/architecture.md, etc.) instead of the pre-Phase-2
flat layout.

Verified: all 24 ci-guards/*.sh pass locally; qa-doc-seed-count.sh
clean. Net diff: 178 additions / 112 deletions across 13 files.
One file deleted (qa-doc-part-count.sh) and one file added
(docs/reference/configuration.md).

Makefile

@@ -119,15 +119,18 @@ verify:
 	@echo ""
 	@echo "verify: PASS — safe to commit"
 
-# verify-docs: pre-tag gate. Runs the QA-doc Part-count + seed-count
-# drift guards that ci-pipeline-cleanup Phase 11 / frozen decision 0.13
-# moved out of CI (was per-push blocking; now operator-runs pre-tag).
-# These guards protect docs/qa-test-guide.md headlines from drifting
-# vs the underlying source-of-truth (testing-guide Part count, seed
-# row count). Operator-facing docs only — not product-affecting.
+# verify-docs: pre-tag gate. Runs the QA-doc seed-count drift guard
+# that ci-pipeline-cleanup Phase 11 / frozen decision 0.13 moved out
+# of CI (was per-push blocking; now operator-runs pre-tag). Protects
+# docs/contributor/qa-test-suite.md::Seed Data Reference from
+# drifting vs migrations/seed_demo.sql. Operator-facing docs only —
+# not product-affecting.
+#
+# The QA-doc Part-count drift guard retired in the 2026-05-04 docs
+# overhaul Phase 5 when docs/testing-guide.md was pruned (its content
+# dispersed across the audience-organized doc tree); the Part-count
+# class no longer exists outside the qa_test.go file itself.
 verify-docs:
-	@echo "==> QA-doc Part-count drift"
-	@bash scripts/qa-doc-part-count.sh
 	@echo "==> QA-doc seed-count drift"
 	@bash scripts/qa-doc-seed-count.sh
 	@echo ""
@@ -263,9 +266,12 @@ frontend-build:
 	@echo "Frontend build complete"
 
 # QA Suite Stats — Bundle P / Strengthening #8.
-# Single source-of-truth for every count claim in docs/qa-test-guide.md +
-# docs/testing-guide.md. The Strengthening #6 CI drift guards consume the
-# same numbers, eliminating the doc-drift class structurally.
+# Single source-of-truth for every count claim in
+# docs/contributor/qa-test-suite.md. The Strengthening #6 CI drift guards
+# (now scoped to the seed-count class only — the Part-count class retired
+# in the 2026-05-04 docs overhaul Phase 5 when testing-guide.md was
+# pruned) consume the same numbers, eliminating the doc-drift class
+# structurally.
 qa-stats:
 	@echo "=== certctl QA Suite Stats ==="
 	@echo "Date: $$(date +%Y-%m-%d)"
@@ -278,7 +284,6 @@ qa-stats:
 	@echo "Fuzz targets: $$(grep -rE 'func Fuzz[A-Z]' --include='*_test.go' . 2>/dev/null | wc -l | tr -d ' ')"
 	@echo "t.Skip sites: $$(grep -rE 't\.Skip(Now|f)?\(' --include='*_test.go' . 2>/dev/null | wc -l | tr -d ' ')"
 	@echo "qa_test.go Part_ subtests: $$(grep -cE 't\.Run\(\"Part[0-9]+_' deploy/test/qa_test.go 2>/dev/null || echo 0)"
-	@echo "testing-guide.md Parts: $$(grep -cE '^## Part [0-9]+:' docs/testing-guide.md 2>/dev/null || echo 0)"
 	@echo "Seed unique mc-* IDs:  $$(grep -oE "mc-[a-z0-9_-]+" migrations/seed_demo.sql 2>/dev/null | sort -u | wc -l | tr -d ' ')"
 	@echo "Seed unique ag-* IDs:  $$(grep -oE "ag-[a-z0-9_-]+" migrations/seed_demo.sql 2>/dev/null | sort -u | wc -l | tr -d ' ') (incl. agent_groups; agents-table count is 12)"
 	@echo "Seed unique iss-* IDs: $$(grep -oE "iss-[a-z0-9_-]+" migrations/seed_demo.sql 2>/dev/null | sort -u | wc -l | tr -d ' ') (issuers table count is 13)"