fix: maintain stable file IDs on re-indexing

[echobt]

Description

This PR addresses an issue where file IDs were changing upon re-indexing, breaking data integrity. The issue was caused by the use of INSERT OR REPLACE, which deletes the existing row and creates a new one with a new auto-incremented ID.

Changes

• Replaced INSERT OR REPLACE with INSERT ... ON CONFLICT(path) DO UPDATE SET ... (UPSERT) in insert_file().
• This ensures that if a file with the same path already exists, its ID is preserved while updating its hash and indexed timestamp.
• Explicitly fetching the ID after upsert to ensure correctness across SQLite versions/drivers.

Validation

• Verified with a reproduction test case that file IDs remain constant after re-inserting the same file with a different hash.
• Ran existing tests to ensure no regressions.