Fix #1500: Document duplicate PR prevention system

Issue #1500 observed that the pre-flight check successfully prevented
a duplicate PR for #1474. This documentation explains the system.

Documents:
- Pre-flight check workflow
- Cleanup scripts
- Best practices
- Troubleshooting

Refs #1500

docs/duplicate-pr-prevention.md

@@ -0,0 +1,89 @@
+# Duplicate PR Prevention System
+
+## Overview
+
+The Nexus uses a multi-layer system to prevent duplicate PRs for the same issue.
+
+## Components
+
+### 1. Pre-flight Check (CI)
+
+The `.github/workflows/pr-duplicate-check.yml` workflow runs on every PR creation and checks if a PR already exists for the same issue.
+
+**How it works:**
+1. Extracts issue numbers from PR title and body
+2. Queries Gitea API for existing PRs referencing those issues
+3. Fails the check if duplicates are found
+4. Provides links to existing PRs for review
+
+### 2. Cleanup Script
+
+The `scripts/cleanup-duplicate-prs.sh` script helps clean up existing duplicates:
+- Lists all PRs for a given issue
+- Identifies duplicates
+- Provides commands to close duplicates
+
+### 3. Milestone Checker
+
+The `bin/check_duplicate_milestones.py` script prevents duplicate milestones:
+- Scans all milestones in the repo
+- Identifies duplicates by title
+- Reports for manual cleanup
+
+## Usage
+
+### Check for Duplicates Before Creating PR
+
+```bash
+# Check if issue already has PRs
+curl -s -H "Authorization: token $GITEA_TOKEN" \
+  "https://forge.alexanderwhitestone.com/api/v1/repos/Timmy_Foundation/the-nexus/pulls?state=open" \
+  | jq '.[] | select(.body | contains("#ISSUE_NUMBER"))'
+```
+
+### Clean Up Existing Duplicates
+
+```bash
+# List PRs for issue
+./scripts/cleanup-duplicate-prs.sh --issue 1128
+
+# Close duplicates (keep newest)
+./scripts/cleanup-duplicate-prs.sh --issue 1128 --close-duplicates
+```
+
+## Example: Issue #1500
+
+Issue #1500 documented that the pre-flight check successfully prevented a duplicate PR for #1474.
+
+**What happened:**
+1. Dispatch attempted to work on #1474
+2. Pre-flight check found 2 existing PRs (#1495, #1493)
+3. System prevented creating a 3rd duplicate
+4. Issue #1500 was filed as an observation
+
+**Result:** The system worked as intended.
+
+## Best Practices
+
+1. **Always check before creating PRs** — use the pre-flight check
+2. **Close duplicates promptly** — don't let them accumulate
+3. **Reference issues in PRs** — makes duplicate detection possible
+4. **Use descriptive branch names** — helps identify purpose
+5. **Review existing PRs first** — don't assume you're the first
+
+## Troubleshooting
+
+### "Duplicate PR detected" error
+
+This means a PR already exists for the issue. Options:
+1. Review the existing PR and contribute to it
+2. Close your PR if it's truly a duplicate
+3. Update your PR to address a different aspect
+
+### Pre-flight check not running
+
+Check that `.github/workflows/pr-duplicate-check.yml` exists and is enabled.
+
+### False positives
+
+The check looks for issue numbers in PR body. If you're referencing an issue without intending to fix it, use "Refs #" instead of "Fixes #".