fix: Use global branch numbering instead of per-short-name numbering (Issue #34)

[kanfil]

Summary

Fixes the bug where spec.specify creates multiple branches with the same 001 prefix when creating different features.

Problem

The AI instructions in templates/commands/specify.md were telling the agent to:

1. Only search for branches matching the exact short-name pattern (e.g., *-user-auth)
2. If no matching branches found, start with number 1

This caused the following scenario:

• Create 001-user-auth
• Create 001-payment-gateway (DUPLICATE - should be 002)
• Create 001-analytics-dashboard (DUPLICATE - should be 003)

Solution

Remove the AI pre-calculation of branch numbers and let the bash script handle numbering automatically. The script already has the correct global numbering logic in:

• get_highest_from_branches() - checks ALL branches regardless of short-name
• check_existing_branches() - combines branches and specs to find the next global number

Before (broken)

b. Find the highest feature number across all sources for the short-name:
   - Remote branches: `git ls-remote --heads origin | grep -E 'refs/heads/[0-9]+-<short-name>$'`
   ...
   - If no existing branches/directories found with this short-name, start with number 1

After (fixed)

Run the script `{SCRIPT}` with the short-name, mode, and options. The script will automatically 
determine the next available global number by checking ALL existing branches and specs.

- Do NOT pass `--number` - let the script auto-detect the next global number

Related Issues

• Closes [Bug]: spec.specify creates multiple branches with 001 prefix #34 (this fork)
• Upstream issues: bug: automatic branch naming repeats numbering prefix such as 001-second-branch after 001-first-branch github/spec-kit#1066, 10th spec given same name as first spec github/spec-kit#1332, The name of branch created by speckit.specify github/spec-kit#1454
• Aligned with: resolves #1454 - remove branch numbering logic from template github/spec-kit#1466 (similar approach)

Testing

After this fix:

• Create 001-user-auth
• Create 002-payment-gateway (correct!)
• Create 003-analytics-dashboard (correct!)

[github-actions]

⚠️ No evaluation results found

[github-actions]

📊 Eval Results

Overall: 7/25 tests passed (28%)

Metric	Value
✅ Passed	7
❌ Failed	18
📈 Pass Rate	28%
🪙 Total Tokens	121,022
💾 Cached Tokens	0

❌ Failed Tests

• Unknown (score: 0.86)
• Unknown (score: 0.83)
• Unknown (score: 0.80)
• Unknown (score: 0.80)
• Unknown (score: 0.78)
• Unknown (score: 0.79)
• Unknown (score: 0.86)
• Unknown (score: 0.89)
• Unknown (score: 0.71)
• Unknown (score: 0.83)
• Unknown (score: 0.83)
• Unknown (score: 0.89)
• Unknown (score: 0.83)
• Unknown (score: 0.68)
• Unknown (score: 0.68)
• Unknown (score: 0.95)
• Unknown (score: 0.87)
• Unknown (score: 0.79)

⚠️ Quality thresholds not met (target: 85%). Please review failures.