docs(#3552): add mode-dependent configure() options guidance

[fullsend-ai-coder]

Add a new Mode-Dependent configure() Options subsection to the E2E Testing section of AGENTS.md, placed after the Plugin Metadata Resolution table.

Documents two configure() options with mode-dependent behavior:

• disablePlugins: only effective in PR and local dev modes where
  auto-generation runs; silently ignored in nightly mode. Advises
  against unnecessary conditional guards since the option is
  already a no-op in nightly mode.

• dynamicPlugins: has destructive side effects in nightly mode
  (generates disabled:true for baked-in plugins). Documents when
  a mode guard is needed vs not. Cross-references Add AGENTS.md guidance for baked-in plugin E2E test configuration #3112 for
  baked-in plugin guidance.

Includes review guidance for agents to flag unnecessary mode guards around disablePlugins and missing mode guards around dynamicPlugins.

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Closes #3552

Post-script verification

• Branch is not main/master (agent/3552-configure-mode-guidance)
• Secret scan passed (gitleaks — de1e7b92a96b94cc158cb2e943995ebbe1adde18..HEAD)
• Pre-commit hooks passed (authoritative run on runner)
• Tests ran inside sandbox

[openshift-ci]

Hi @fullsend-ai-coder[bot]. Thanks for your PR.

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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[fullsend-ai-review]

🤖 Finished Review · ✅ Success · Started 3:27 PM UTC · Completed 3:44 PM UTC

Commit: c3f0429 · View workflow run →

Runtime: claude · Model: opus → claude-opus-4-6 · Cost: $4.52

[fullsend-ai-review]

Review

Findings

Medium

• [internal-consistency] AGENTS.md — The prose states that disablePlugins "only has effect in PR mode (when GIT_PR_NUMBER is set)" but the table immediately below lists Local dev mode as also having the effect (Auto-generation runs: Yes, disablePlugins effect: "Removes named plugins from generated config"). The same sentence confirms both modes: "auto-generation only runs in PR and local dev modes." The bold claim contradicts both the table and the supporting sentence.
  Remediation: Change "It only has effect in PR mode" to "It only has effect when auto-generation runs (PR and local dev modes)" or equivalently "It has no effect in nightly mode".

• [protected-path] AGENTS.md — This file is a protected path requiring human approval. The PR links to issue Add AGENTS.md guidance for configure() option mode dependencies beyond dynamicPlugins #3552 and explains the rationale for the change. Human approval is always required for protected-path changes, regardless of context.

Low

• [internal-consistency] AGENTS.md — The new section claims auto-generation only runs in PR and local dev modes, but existing lines 287 and 316 describe auto-generation without mode qualifiers, which could confuse readers. Consider adding a mode qualifier parenthetical to those lines (e.g., "auto-generates from metadata/*.yaml if no dynamic-plugins.yaml exists (in PR and local dev modes)").

• [document-structure-consistency] AGENTS.md — The new section introduces #### headings (#### disablePlugins, #### dynamicPlugins, #### Review guidance), but the rest of the file exclusively uses a flat ##/### heading hierarchy (33 existing ### subsections, zero ####). Consider flattening to bold text sub-topics within the ### Mode-Dependent configure() Options section, matching the approach used elsewhere in the file.

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Labels: PR modifies only AGENTS.md documentation outside workspace directories.