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fix: convert shell syntax to array args in 4 more tools (#302)#311

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TerminalGravity wants to merge 3 commits intomainfrom
fix/shell-syntax-302-round5
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fix: convert shell syntax to array args in 4 more tools (#302)#311
TerminalGravity wants to merge 3 commits intomainfrom
fix/shell-syntax-302-round5

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Fixes shell syntax being passed to run() (which uses execFileSync without a shell) in 4 tools:

  • sharpen-followup: 3 diff commands + status → array args
  • sequence-tasks: ls-files → array args
  • session-handoff: replaced run() with execFileSync for non-git commands (which, gh), added runExternal() helper
  • checkpoint: split shell-chained add && commit into separate run() calls with array args

All tests pass, clean tsc build.

Ref: #302

The interactive setup wizard (npx preflight-dev init) was buried in a
footnote under Option C, despite being the most user-friendly onboarding
path. Moved it to Option A with a clear description of what it does.
Renumbered remaining options accordingly.
The README and examples/README.md both referenced examples/.preflight/
but the directory didn't exist. Adds:
- config.yml — profile, related projects, thresholds, embeddings
- triage.yml — keyword rules, strictness, cross-service triggers
- contracts/api.yml — manual contract definitions with realistic examples

All files have detailed comments explaining every option.
- sharpen-followup: convert diff/status calls to array args
- sequence-tasks: convert ls-files to array args
- session-handoff: add runExternal() for non-git commands
- checkpoint: split shell-chained add+commit into separate calls

Ref: #302
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