Fix atomic writes and fs.constants flags in InitCommand and ConfigService

[Copilot]

Description

Three issues with config file writes: a TypeScript build failure from using non-existent fs.O_CREAT/O_EXCL/O_RDWR (should be fs.constants.*), a missing try/finally that could leak file descriptors, and non-atomic writeFileSync calls in both the backup/overwrite branches and ConfigService.saveConfig() that risk file corruption on interruption.

src/commands/InitCommand.ts

• fs.O_CREAT | fs.O_EXCL | fs.O_RDWR → fs.constants.O_CREAT | fs.constants.O_EXCL | fs.constants.O_RDWR (fixes CI build)
• Wrapped writeFileSync/fsyncSync in try/finally to guarantee fd is always closed
• Added atomicWriteFileSync helper: opens a .tmp-<pid>-<ts> file in the same directory with O_CREAT | O_EXCL | O_WRONLY, writes, fsyncs, closes, then renameSyncs into place; cleans up temp on rename failure
• Both backup-then-replace and overwrite branches now use atomicWriteFileSync

src/services/ConfigService.ts

• saveConfig() rewritten with the same temp-file + fsync + rename pattern, consistent temp naming (.tmp-<pid>-<ts> in config directory)

// Before — non-atomic, can corrupt on interruption
fs.writeFileSync(configPath, JSON.stringify(validated, null, 2), { mode: 0o600 });

// After — atomic
const tempPath = path.join(path.dirname(configPath), `.tmp-${process.pid}-${Date.now()}`);
const fd = fs.openSync(tempPath, fs.constants.O_CREAT | fs.constants.O_EXCL | fs.constants.O_WRONLY, 0o600);
try {
  fs.writeFileSync(fd, JSON.stringify(validated, null, 2));
  fs.fsyncSync(fd);
} finally {
  fs.closeSync(fd);
}
fs.renameSync(tempPath, configPath);

Related Issue

Closes #

Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)
• ✨ New feature (non-breaking change that adds functionality)
• 💥 Breaking change (fix or feature that would cause existing functionality to change)
• 📝 Documentation update
• 🔧 Refactor / internal improvement
• 🤖 CI/CD or tooling change
• ⬆️ Dependency update

Checklist

• I have read the CONTRIBUTING guidelines (if present)
• My code follows the existing code style
• I have added or updated tests that cover my changes
• All existing tests pass locally
• I have updated the documentation where necessary
• My changes do not introduce new security vulnerabilities

How Has This Been Tested?

npm run build (previously failing, now passes) and npm test (lint + tsc --noEmit). CodeQL returned 0 alerts.

Screenshots (if applicable)

Additional Notes

The atomic write pattern mirrors the existing ConflictResolver.applyResolution() already in the codebase. Temp files are created in the same directory as the target to ensure rename is a same-filesystem operation.

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