fix(api): honor linked project root directory

[swingo35]

What changed

• honor a project's configured rootDirectory when resolving Compose drift from GitHub
• reject a missing configured root instead of silently reconciling an unrelated repository root
• clear stale local source paths when a local project is linked to GitHub, including sibling environments
• add coverage for selecting an explicit nested Compose root when the repository also has a root Compose file

Why

An adopted local Compose project can be linked to a GitHub repository whose deployment manifest lives in a subdirectory. Previously, the link kept localPath, while drift reconciliation auto-detected the repository root and could import unrelated services. This makes the linked GitHub repository and configured root the actual deployment source.

Validation

• bun run --cwd apps/api test -- test/modules/deployments/prepare.service.test.ts
• bun run --cwd apps/api lint
• git diff --check

[Hydralerne]

are we fine to merge ?