feat(agents): add thinking model guidance reference files (#1722) (#1820)

Combines implementation by @davesienkowski (inline @-reference wiring at
decision-point steps, named reasoning models with anti-patterns, sequencing
rules, Gap Closure Mode) and @Tibsfox (test suite covering file existence,
section structure, and agent wiring).

- 5 reference files in get-shit-done/references/ — each with named reasoning
  models, Counters annotations, Conflict Resolution sequencing, and When NOT
  to Think guidance
- Inline @-reference wiring placed inside the specific step/section blocks
  where thinking decisions occur (not at top-of-agent)
- Planning cluster includes Gap Closure Mode root-cause check section
- Test suite: 63 tests covering file existence, named models, Conflict
  Resolution sections, Gap Closure Mode, and inline wiring placement

Closes #1722

Co-authored-by: Tibsfox <tibsfox@users.noreply.github.com>
Co-authored-by: Rezolv <davesienkowski@users.noreply.github.com>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

agents/gsd-debugger.md

@@ -957,6 +957,9 @@ Gather symptoms through questioning. Update file after EACH answer.
 </step>
 
 <step name="investigation_loop">
+At investigation decision points, apply structured reasoning:
+@~/.claude/get-shit-done/references/thinking-models-debug.md
+
 **Autonomous investigation. Update file continuously.**
 
 **Phase 0: Check knowledge base**

agents/gsd-executor.md

@@ -95,6 +95,9 @@ grep -n "type=\"checkpoint" [plan-path]
 </step>
 
 <step name="execute_tasks">
+At execution decision points, apply structured reasoning:
+@~/.claude/get-shit-done/references/thinking-models-execution.md
+
 For each task:
 
 1. **If `type="auto"`:**

agents/gsd-phase-researcher.md

@@ -461,6 +461,9 @@ Verified patterns from official sources:
 
 <execution_flow>
 
+At research decision points, apply structured reasoning:
+@~/.claude/get-shit-done/references/thinking-models-research.md
+
 ## Step 1: Receive Scope and Load Context
 
 Orchestrator provides: phase number/name, description/goal, requirements, constraints, output path.

agents/gsd-plan-checker.md

@@ -80,6 +80,9 @@ Same methodology (goal-backward), different timing, different subject matter.
 
 <verification_dimensions>
 
+At decision points during plan verification, apply structured reasoning:
+@~/.claude/get-shit-done/references/thinking-models-planning.md
+
 ## Dimension 1: Requirement Coverage
 
 **Question:** Does every phase requirement have task(s) addressing it?

agents/gsd-planner.md

@@ -1022,6 +1022,9 @@ cat "$phase_dir"/*-DISCOVERY.md 2>/dev/null  # From mandatory discovery
 </step>
 
 <step name="break_into_tasks">
+At decision points during plan creation, apply structured reasoning:
+@~/.claude/get-shit-done/references/thinking-models-planning.md
+
 Decompose phase into tasks. **Think dependencies first, not sequence.**
 
 For each task:

agents/gsd-verifier.md

@@ -57,6 +57,9 @@ Then verify each level against the actual codebase.
 
 <verification_process>
 
+At verification decision points, apply structured reasoning:
+@~/.claude/get-shit-done/references/thinking-models-verification.md
+
 ## Step 0: Check for Previous Verification
 
 ```bash