feat: v3.0.0 architecture overhaul

- Rename marketplace to lm-claude-plugins
- Move MCP servers to root with symlinks
- Add 6 PR tools to Gitea MCP (list_pull_requests, get_pull_request,
  get_pr_diff, get_pr_comments, create_pr_review, add_pr_comment)
- Add clarity-assist plugin (prompt optimization with ND accommodations)
- Add git-flow plugin (workflow automation)
- Add pr-review plugin (multi-agent review with confidence scoring)
- Centralize configuration docs
- Update all documentation for v3.0.0

BREAKING CHANGE: MCP server paths changed, marketplace renamed

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

plugins/pr-review/skills/review-patterns/confidence-scoring.md

@@ -0,0 +1,139 @@
+# Confidence Scoring for PR Review
+
+## Purpose
+
+Confidence scoring ensures that review findings are calibrated and actionable. By filtering out low-confidence findings, we reduce noise and focus reviewer attention on real issues.
+
+## Score Ranges
+
+| Range | Label | Meaning | Action |
+|-------|-------|---------|--------|
+| 0.9 - 1.0 | HIGH | Definite issue | Must address |
+| 0.7 - 0.89 | MEDIUM | Likely issue | Should address |
+| 0.5 - 0.69 | LOW | Possible concern | Consider addressing |
+| < 0.5 | SUPPRESSED | Uncertain | Don't report |
+
+## Scoring Factors
+
+### Positive Factors (Increase Confidence)
+
+| Factor | Impact |
+|--------|--------|
+| Clear data flow from source to sink | +0.3 |
+| Pattern matches known vulnerability | +0.2 |
+| No intervening validation visible | +0.2 |
+| Matches OWASP Top 10 | +0.15 |
+| Found in security-sensitive context | +0.1 |
+
+### Negative Factors (Decrease Confidence)
+
+| Factor | Impact |
+|--------|--------|
+| Validation might exist elsewhere | -0.2 |
+| Depends on runtime configuration | -0.15 |
+| Pattern is common but often safe | -0.15 |
+| Requires multiple conditions to exploit | -0.1 |
+| Theoretical impact only | -0.1 |
+
+## Calibration Guidelines
+
+### Security Issues
+
+Base confidence by pattern:
+- SQL string concatenation with user input: 0.95
+- Hardcoded credentials: 0.9
+- Missing auth check: 0.8
+- Generic error exposure: 0.6
+- Missing rate limiting: 0.5
+
+### Performance Issues
+
+Base confidence by pattern:
+- Clear N+1 in loop: 0.9
+- SELECT * on large table: 0.7
+- Missing index on filtered column: 0.6
+- Suboptimal algorithm: 0.5
+
+### Maintainability Issues
+
+Base confidence by pattern:
+- Function >100 lines: 0.8
+- Deep nesting >4 levels: 0.75
+- Duplicate code blocks: 0.7
+- Unclear naming: 0.6
+- Minor style issues: 0.3 (suppress)
+
+### Test Coverage
+
+Base confidence by pattern:
+- No test file for new module: 0.9
+- Security function untested: 0.85
+- Edge case not covered: 0.6
+- Simple getter untested: 0.3 (suppress)
+
+## Threshold Configuration
+
+The default threshold is 0.5. This can be adjusted:
+
+```bash
+PR_REVIEW_CONFIDENCE_THRESHOLD=0.7  # Only high-confidence
+PR_REVIEW_CONFIDENCE_THRESHOLD=0.3  # Include more speculative
+```
+
+## Example Scoring
+
+### High Confidence (0.95)
+
+```javascript
+// Clear SQL injection
+const query = `SELECT * FROM users WHERE id = ${req.params.id}`;
+```
+
+- User input (req.params.id): +0.3
+- Direct to SQL query: +0.3
+- No visible validation: +0.2
+- Matches OWASP Top 10: +0.15
+- **Total: 0.95**
+
+### Medium Confidence (0.72)
+
+```javascript
+// Possible performance issue
+users.forEach(async (user) => {
+  const orders = await db.orders.find({ userId: user.id });
+});
+```
+
+- Loop with query: +0.3
+- Pattern matches N+1: +0.2
+- But might be small dataset: -0.15
+- Could have caching: -0.1
+- **Total: 0.72**
+
+### Low Confidence (0.55)
+
+```javascript
+// Maybe too complex?
+function processOrder(order, user, items, discounts, shipping) {
+  // 60 lines of logic
+}
+```
+
+- Function is long: +0.2
+- Many parameters: +0.15
+- But might be intentional: -0.1
+- Could be refactored later: -0.1
+- **Total: 0.55**
+
+### Suppressed (0.35)
+
+```javascript
+// Minor style preference
+const x = foo ? bar : baz;
+```
+
+- Ternary could be if/else: +0.1
+- Very common pattern: -0.2
+- No real impact: -0.1
+- Style preference: -0.1
+- **Total: 0.35** (suppressed)