feat: configurable setup script timeout (CYPACK-1080)

[cyrusagent]

Assignee: @Connoropolous (connor)

Summary

Setup scripts previously had a hard-coded 5-minute timeout, which is too short for steps like a full database restore. Introduces per-repo and global overrides in ~/.cyrus/config.json.

Fixes CYPACK-1080 (GitHub issue #1102).

Changes

• setupScriptTimeoutMs (number, per-repo) — timeout in milliseconds for the repository setup script (cyrus-setup.sh/.ps1/.cmd/.bat). Added to RepositoryConfig.
• global_setup_script_timeout_ms (number, top-level) — timeout in milliseconds for the global setup script. Added to EdgeConfig.
• Both default to 300000 (5 minutes), so unchanged configs behave exactly as before.
• Timeout-exceeded log message now reports the actual timeout instead of hard-coding "5 minutes".

Implementation

• packages/core/src/config-schemas.ts: added both Zod fields; JSON schemas regenerated.
• packages/edge-worker/src/GitService.ts: runSetupScript and runRepoSetupScript now accept a timeoutMs parameter; CreateGitWorktreeOptions.globalSetupScriptTimeoutMs is threaded through createGitWorktree → createSingleRepoWorktree → runSetupScript; per-repo timeout is read from repository.setupScriptTimeoutMs.
• apps/cli/src/services/WorkerService.ts: forwards edgeConfig.global_setup_script_timeout_ms into createGitWorktree.
• docs/SETUP_SCRIPTS.md, docs/CONFIG_FILE.md: documented both new fields with JSON examples.

Test plan

• New unit tests in packages/edge-worker/test/GitService.test.ts cover:
  • default 5-minute timeout when no override is set
  • globalSetupScriptTimeoutMs option is honored for the global setup script
  • repository.setupScriptTimeoutMs is honored for the per-repo setup script
• pnpm test:packages:run — all 571 edge-worker tests pass
• pnpm typecheck — clean across all packages
• pnpm biome check — no new warnings introduced
• JSON schema sync test passes (schemas regenerated from Zod)

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