fix: remove shell syntax from run() in checkpoint, sharpen-followup, sequence-tasks, session-handoff (#302)

[TerminalGravity]

Fixes 4 more tools affected by #302 (shell syntax passed to run() which uses execFileSync without a shell).

Changes:

• checkpoint.ts: Replaced shell-chained git add && git commit with separate run() array calls; inlined staging logic instead of building a shell command string
• sharpen-followup.ts: Converted 4 run() calls from shell strings with 2>/dev/null to proper arrays
• sequence-tasks.ts: Replaced git ls-files 2>/dev/null | head -1000 with array args + JS .slice(0, 1000)
• session-handoff.ts: Replaced command -v (shell builtin) with which via execFileSync; replaced gh pr list ... 2>/dev/null || echo '[]' with direct execFileSync + try/catch

All changes compile clean (tsc --noEmit passes).

[TerminalGravity]

Reviewed — this looks solid. The checkpoint refactor replacing shell-chained addCmd && git commit with separate run() calls is cleaner. The hasCommand switch to which via execFileSync is correct since command -v is a shell builtin. The head -1000 → JS .slice(0, 1000) in sequence-tasks is a nice touch.

One thing to double-check: in checkpoint.ts the error detection changed from commit failed to command failed — make sure run() actually returns that prefix on failure, otherwise the rollback path won't trigger and you'll silently swallow commit errors.