fix(hooks): remove all venv auto-repair code that deleted .venv directories

BREAKING: Removes automatic venv management that was causing session failures

Changes:
- Delete scripts/venv-repair.sh (was deleting and recreating venvs)
- Remove auto-repair code from projman/hooks/startup-check.sh
- Remove venv-repair call from scripts/post-update.sh
- Remove rm -rf .venv instructions from docs/UPDATING.md and CONFIGURATION.md
- Update docs/CANONICAL-PATHS.md to remove venv-repair.sh reference

Additionally:
- Add Pre-Change Protocol to CLAUDE.md (mandatory dependency check before edits)
- Add Pre-Change Protocol enforcement to claude-config-maintainer plugin
- Add Development Context section to CLAUDE.md clarifying which plugins are
  used in this project vs only being developed
- Reorganize commands table to separate relevant vs non-relevant commands

The venv auto-repair was the root cause of repeated MCP server failures,
requiring manual setup.sh runs after every session start.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

plugins/claude-config-maintainer/commands/analyze.md

@@ -59,6 +59,7 @@ Analyze the CLAUDE.md file in this project
 - Quick start commands documented
 - Critical rules highlighted
 - Key workflows covered
+- **Pre-Change Protocol section present** (MANDATORY - see below)
 
 ### Conciseness (25 points)
 - No unnecessary repetition
@@ -66,6 +67,42 @@ Analyze the CLAUDE.md file in this project
 - Appropriate length for project size
 - No generic filler content
 
+## Pre-Change Protocol Check (MANDATORY)
+
+**This check is CRITICAL.** The Pre-Change Protocol section ensures Claude performs comprehensive dependency analysis before making any code changes, preventing missed references and incomplete updates.
+
+### What to Check
+
+Search CLAUDE.md for:
+- Section header containing "Pre-Change" or "Before Any Code Change"
+- References to `grep -rn` or impact search
+- Checklist with "Files That Will Be Affected"
+- Requirement for user verification before proceeding
+
+### If Missing
+
+**Flag as HIGH PRIORITY issue:**
+
+```
+1. [HIGH] Missing Pre-Change Protocol section
+   CLAUDE.md lacks mandatory dependency-check protocol.
+   Impact: Claude may miss file references when making changes,
+   leading to broken dependencies and incomplete updates.
+
+   Recommendation: Add Pre-Change Protocol section immediately.
+   This is the #1 cause of cascading bugs from incomplete changes.
+```
+
+### Required Section Content
+
+The Pre-Change Protocol section must include:
+1. Requirement to run grep search and show results
+2. List of files that will be affected
+3. List of files searched but not changed (with reasoning)
+4. Documentation that references the change target
+5. User verification checkpoint before proceeding
+6. Post-change verification step
+
 ## Plugin Integration Analysis
 
 After the content analysis, the command detects and analyzes marketplace plugin integration:

plugins/claude-config-maintainer/commands/init.md

@@ -139,6 +139,7 @@ For small projects or when starting fresh:
 - Project Overview (required)
 - Quick Start (required)
 - Critical Rules (required)
+- **Pre-Change Protocol (required)**
 
 ### Standard Template (default)
 For typical projects:
@@ -146,6 +147,7 @@ For typical projects:
 - Quick Start
 - Architecture
 - Critical Rules
+- **Pre-Change Protocol**
 - Common Operations
 - File Structure
 
@@ -153,11 +155,44 @@ For typical projects:
 For large or complex projects:
 - All standard sections plus:
 - Detailed Architecture
+- **Pre-Change Protocol**
 - Troubleshooting
 - Integration Points
 - Development Workflow
 - Deployment Notes
 
+### Pre-Change Protocol Section (MANDATORY in ALL templates)
+
+**This section MUST be included in every generated CLAUDE.md:**
+
+```markdown
+## ⛔ MANDATORY: Before Any Code Change
+
+**Claude MUST show this checklist BEFORE editing any file:**
+
+### 1. Impact Search Results
+Run and show output of:
+\`\`\`bash
+grep -rn "PATTERN" --include="*.sh" --include="*.md" --include="*.json" --include="*.py" | grep -v ".git"
+\`\`\`
+
+### 2. Files That Will Be Affected
+Numbered list of every file to be modified, with the specific change for each.
+
+### 3. Files Searched But Not Changed (and why)
+Proof that related files were checked and determined unchanged.
+
+### 4. Documentation That References This
+List of docs that mention this feature/script/function.
+
+**User verifies this list before Claude proceeds. If Claude skips this, stop immediately.**
+
+### After Changes
+Run the same grep and show results proving no references remain unaddressed.
+```
+
+**Rationale:** This protocol prevents incomplete changes where Claude modifies some files but misses others that reference the same code, causing cascading bugs.
+
 ## Auto-Detection
 
 The command automatically detects:

plugins/claude-config-maintainer/commands/optimize.md

@@ -56,6 +56,7 @@ Or specify specific optimizations:
 
 ### Enhance
 - Add missing essential sections
+- **Add Pre-Change Protocol if missing (HIGH PRIORITY)**
 - Improve unclear instructions
 - Add helpful examples
 - Highlight critical rules
@@ -158,6 +159,49 @@ Backup saved to: .claude/backups/CLAUDE.md.2025-01-18
 | `--preserve-comments` | Keep all existing comments |
 | `--section=NAME` | Optimize specific section only |
 
+## Pre-Change Protocol (Mandatory Addition)
+
+**If CLAUDE.md is missing the Pre-Change Protocol section, optimization MUST add it.**
+
+This is the highest priority enhancement because it prevents cascading bugs from incomplete code changes.
+
+### Detection
+
+Search CLAUDE.md for:
+- "Pre-Change" or "Before Any Code Change" in headers
+- References to impact search or grep verification
+- User verification checkpoint
+
+### If Missing
+
+Add this section (position: after Critical Rules, before Common Operations):
+
+```markdown
+## ⛔ MANDATORY: Before Any Code Change
+
+**Claude MUST show this checklist BEFORE editing any file:**
+
+### 1. Impact Search Results
+Run and show output of:
+\`\`\`bash
+grep -rn "PATTERN" --include="*.sh" --include="*.md" --include="*.json" --include="*.py" | grep -v ".git"
+\`\`\`
+
+### 2. Files That Will Be Affected
+Numbered list of every file to be modified, with the specific change for each.
+
+### 3. Files Searched But Not Changed (and why)
+Proof that related files were checked and determined unchanged.
+
+### 4. Documentation That References This
+List of docs that mention this feature/script/function.
+
+**User verifies this list before Claude proceeds. If Claude skips this, stop immediately.**
+
+### After Changes
+Run the same grep and show results proving no references remain unaddressed.
+```
+
 ## When to Use
 
 Run `/config-optimize` when: