Unify default repo/queue base-dir resolution (avoid CWD/project-root split)

[kapral18]

Problem

The CLI currently uses different default roots for related runtime state:

• Repository clones for URL/repo-name inputs are rooted at process.cwd() (.repos/...) in setup and index flows.
• Queue state defaults to project root via SCSI_QUEUE_BASE_DIR resolution in config.

This can split state when commands are run from a different working directory (for example cron/job runners), causing repos and queue DBs to land in different base locations.

Why this is risky

• Duplicate clones can be created across different CWDs.
• Queue/recovery operations become harder to reason about.
• Behavior is less predictable for automation and operators.

Current behavior (example)

Running the index command from /tmp can place:

• repos under /tmp/.repos/...
• queues under <project-root>/.queues/...

Proposed direction

Unify default base-dir behavior for repo storage and queue storage.

Possible approach:

1. Introduce a single canonical repos base dir config (for example SCSI_REPOS_BASE_DIR) resolved from project root by default.
2. Use that base in both setup_command and parseRepoArg for URL/repo-name inputs.
3. Keep explicit absolute/relative repo path arguments working as-is.
4. Document the final default behavior in README/DEVELOPER_GUIDE.

Acceptance criteria

• Invoking from different CWDs does not split default repo/queue state across unrelated directories.
• Existing explicit repo-path usage keeps working.
• Unit tests cover repo path resolution for URL/repo-name + explicit paths.

Context

• PR discussion: refactor(config): centralize env vars; fix search CLI #150
• Specifically raised in review threads on:
  • src/commands/setup_command.ts
  • src/commands/index_command.ts

[kapral18]

Adding direct review-comment references from PR #150 for traceability:

• CWD/root consistency comment on setup_command.ts: refactor(config): centralize env vars; fix search CLI #150 (comment)
• CWD/root consistency comment on index_command.ts: refactor(config): centralize env vars; fix search CLI #150 (comment)

Related PR: #150