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).

docs/reference/connectors/adcs.md

@@ -87,10 +87,11 @@ When the certctl sub-CA cert is approaching expiry:
 1. Generate a new keypair (re-keying is recommended at sub-CA
    rotation time).
 2. CSR + ADCS signing cycle as above.
-3. Stage the new cert and key at fresh paths
-   (`CERTCTL_CA_CERT_PATH_NEW` etc.) and follow the
+3. Stage the new cert and key at fresh on-disk paths and follow the
    [intermediate-CA hierarchy
-   runbook](../intermediate-ca-hierarchy.md) for the cutover. The
+   runbook](../intermediate-ca-hierarchy.md) for the cutover (rotate
+   `CERTCTL_CA_CERT_PATH` / `CERTCTL_CA_KEY_PATH` to the new files
+   when ready). The
    key concern is overlap: both the old and new sub-CA certs must
    chain to the ADCS root during the rollover so existing leaves
    keep validating.