CLI init does not deploy full settings.json features from repo

## Summary

The `.claude/settings.json` in the repository (529 lines) contains features that are NOT generated by any `init` command (240 lines). This creates a gap between the reference configuration and what users actually get.

## Missing Features

The following features exist in the repo's `.claude/settings.json` but are NOT generated by `init --full`:

| Feature | In Repo | Generated by CLI |
|---------|---------|------------------|
| `model` (top-level) | ✅ | ❌ |
| `customInstructions` | ✅ | ❌ |
| `env` (30 variables) | ✅ | ❌ |
| `PreCompact` hooks | ✅ | ❌ |
| `checkpointManager` | ✅ | ❌ |
| `githubIntegration` | ✅ | ❌ |

## Reproduction

```bash
# Fresh init produces 240-line settings.json
mkdir test && cd test
npx claude-flow@v3alpha init --full
wc -l .claude/settings.json # 240 lines

# Repo has 529-line settings.json
curl -s https://raw.githubusercontent.com/ruvnet/claude-flow/main/.claude/settings.json | wc -l # 529 lines
```

## Root Cause

The `settings-generator.ts` template doesn't include these features. They appear to have been manually added to the repo's `.claude/settings.json` but never backported to the generator.

## Suggested Fix

1. Update `v3/@claude-flow/cli/src/init/settings-generator.ts` to include all features from the repo's reference settings.json
2. Or add a `--from-repo` flag that pulls the canonical settings directly
3. Consider `init upgrade --settings` to update only settings.json with new features

## Environment

- CLI Version: 3.0.0-alpha.161
- Node: v24.12.0
- Tested both `claude-flow@v3alpha` and `@claude-flow/cli@latest` - same result

## Impact

Users miss out on useful features like:
- `PreCompact` hooks for preserving patterns during context compaction
- Environment variables enabling V3 features (SONA, HNSW, MoE)
- `checkpointManager` for auto-commit
- `githubIntegration` for PR/issue tracking