fix: resolve pre-commit markdownlint issues

- Add trailing newlines to code-analyst.md, context_bootstrap.md, and information-analyst.md
- Convert emphasis-as-heading to blockquote in research-synthesis.md
- Fix bare URL by converting to markdown link in research-synthesis.md
- Add 'text' language specifiers to all fenced code blocks in generate-codebase-context.md and PROGRESS.md

Resolves CodeRabbit review feedback on PR #15

Co-authored-by: Gregg Coppen <[email protected]>

Author: github-actions[bot]

docs/research/codebase-context/code-analyst.md

@@ -279,3 +279,4 @@ You are running in a **subprocess** to do deep code analysis without overwhelmin
 Your findings will be combined with the Information Analyst's findings (from docs) to create complete context.
 
 ```
+

docs/research/codebase-context/context_bootstrap.md

@@ -56,3 +56,4 @@ You operate as the manager orchestrating two specialists:
 - **Code Analyst** – inspects source, dependencies, APIs, data models, integrations; returns summarized findings plus validation questions.
 - **Information Analyst** – reviews documentation artifacts, diagrams, and in-code commentary; returns inventories, rationale evidence, gaps, and conflicts.
   Keep subprocess outputs concise. Integrate their findings into user conversations and documentation.
+

docs/research/codebase-context/information-analyst.md

@@ -282,3 +282,4 @@ You are running in a **subprocess** to do deep information extraction without ov
 Your findings will be combined with the Code Analyst's findings to create complete context. The Code Analyst tells the manager WHAT and HOW from code. You tell the manager WHY from documentation.
 
 Together, you give the manager everything needed to write accurate PRDs, meaningful ADRs with rationale, and complete SYSTEM-OVERVIEW documentation.
+

docs/research/codebase-context/research-synthesis.md

@@ -18,7 +18,7 @@
 
 ### 🎯 Core Philosophy from context_bootstrap.md
 
-**"Code explains HOW the system currently behaves; the user supplies WHAT it is supposed to achieve and WHY choices were made."**
+> "Code explains HOW the system currently behaves; the user supplies WHAT it is supposed to achieve and WHY choices were made."
 
 This is **critical** - it separates:
 
@@ -701,4 +701,4 @@ Ask targeted questions about:
 - **code-analyst.md:** Specialized agent for code analysis
 - **information-analyst.md:** Specialized agent for documentation analysis
 - **context_bootstrap.md:** Manager orchestration pattern
-- **MADR Format:** https://adr.github.io/madr/
+- **MADR Format:** [Architecture Decision Records (MADR)](https://adr.github.io/madr/)

docs/roadmap/PROGRESS.md

@@ -103,7 +103,7 @@ Explicitly flags items needing user validation.
 
 Step-by-step flow examples:
 
-```
+```text
 User Login Flow:
 1. POST /api/auth/login → src/api/routes/auth.ts:23
 2. AuthController.login() → src/controllers/AuthController.ts:45
@@ -149,7 +149,7 @@ Pre-completion verification:
 
 ### Files Added/Modified
 
-```
+```text
 ✅ prompts/generate-codebase-context.md (enhanced)
 ✅ docs/research/reverse-engineer-prompts/claude-code-feature-dev-comparison.md (new)
 ✅ docs/research/reverse-engineer-prompts/research-synthesis.md (new)

prompts/generate-codebase-context.md

@@ -222,7 +222,7 @@ Trace from entry points to understand:
 
 For key workflows, provide step-by-step execution trace:
 
-```
+```text
 User Login Flow:
 1. POST /api/auth/login → src/api/routes/auth.ts:23
 2. AuthController.login() → src/controllers/AuthController.ts:45
@@ -256,7 +256,7 @@ From dependency files and imports, catalog:
 
 **Evidence format:**
 
-```
+```text
 - **Framework:** React (package.json:15, imports in src/components/*.tsx)
 - **Database:** PostgreSQL (package.json:23 'pg', connection in src/db/pool.ts:8)
 - **Cache:** Redis (docker-compose.yml:34, client in src/cache/redis.ts:12)
@@ -285,7 +285,7 @@ From dependency files and imports, catalog:
 
 Example:
 
-```
+```text
 - **API Service → Database:**
   - Method: Direct ORM queries
   - Evidence: src/services/UserService.ts:45 calls UserRepository.findById()
@@ -348,7 +348,7 @@ For each external integration found:
 
 Example:
 
-```
+```text
 - **Stripe (Payment Processing):**
   - Usage: Charges, subscriptions, webhooks
   - Evidence: src/services/PaymentService.ts:23-156
@@ -403,7 +403,7 @@ Ask 3-5 targeted questions based on gaps found:
 
 Example:
 
-```
+```text
 I found some gaps that need your input:
 
 1. **PostgreSQL vs. MongoDB:**
@@ -426,7 +426,7 @@ I found some gaps that need your input:
 
 **Capture answers as direct quotes:**
 
-```
+```text
 [User confirmed: 2025-01-21: "MongoDB was from an early experiment, it's safe to remove."]
 [User stated: "JWT chosen because we needed stateless auth for mobile clients."]
 ```
@@ -581,7 +581,7 @@ I found some gaps that need your input:
 ### 4.2 Communication Patterns
 
 **API → Services → Repositories → Database:**
-```
+```text
 
 src/api/routes/users.ts:25 (HTTP endpoint)
   → UserService.createUser() (src/services/UserService.ts:67)
@@ -591,7 +591,7 @@ src/api/routes/users.ts:25 (HTTP endpoint)
 ```
 
 **Event-Driven (Async):**
-```
+```text
 
 PaymentService.processCharge() (src/services/PaymentService.ts:89)
   → EventBus.publish('payment.processed') (src/events/bus.ts:23)
@@ -703,7 +703,7 @@ Priority files for anyone working on this codebase:
 
 ### Example 1: User Login
 
-```
+```text
 
 1. User submits credentials via POST /api/auth/login
    Entry: src/api/routes/auth.ts:23
@@ -737,7 +737,7 @@ Priority files for anyone working on this codebase:
 
 ### Example 2: Background Payment Processing
 
-```
+```text
 
 1. Webhook received from Stripe
    Entry: src/api/routes/webhooks/stripe.ts:12
@@ -862,7 +862,6 @@ After this context analysis:
 **Analysis completed:** YYYY-MM-DD
 **Last validated with user:** YYYY-MM-DD
 **Status:** Ready for feature specification
-```
 
 ---