[codex] Preserve repos added after setup

[rushillshah]

Scope

• Preserves repositories already stored in digital-brain.config.json when connect-repos adds explicit paths later.
• Deduplicates repeated paths while retaining insertion order.
• Extends the post-init regression test to cover repeated and additive repository selection.

Partially addresses #3.

Validation

• npm run check
• node --test --test-name-pattern='connect-repos can add repository context after init' tests/cli-init.test.mjs
• npm pack --dry-run
• npm test (65 passed, 4 pre-existing date-sensitive failures reproduced on origin/main; tracked in Tests use stale dated fixtures and fail as time advances #23)

Risk

Low. The merge applies only when explicit repository paths are supplied. Interactive selection behavior is unchanged.

[rushillshah]

Maintenance blocker (2026-07-10): both CI jobs fail on the same four date-sensitive fixture tests reproduced on unchanged origin/main. The focused connect-repos regression passes. Next action: fix #23, then re-run CI; keep this PR draft until checks pass and review is complete.

[rushillshah]

Maintenance update (2026-07-13): the shared date-fixture blocker is fixed in draft PR #25, with npm run check and all 70 tests passing locally. Next action: review/merge #25, then rerun this PR’s CI; keep #24 draft until both checks pass and review is complete.