[CLI] Add support for incremental database migrations

[coderabbitai]

Context

Currently, schema changes to the PDK database (e.g., adding the device_subclass column in PR #2) are handled by deleting the existing database on every pdk scan run. While this ensures the schema is always up-to-date, it prevents incremental scanning and requires full workspace rescans each time.

Desired Behavior

Implement a migration system that:

• Detects existing databases and their schema version
• Applies incremental migrations (e.g., ALTER TABLE statements) to bring older databases up to date
• Preserves existing data during schema updates
• Supports version tracking to enable safe migrations

References

• PR Add StdCell DeviceClass and DeviceSubclass construct #2: Add StdCell DeviceClass and DeviceSubclass construct #2
• Related discussion: Add StdCell DeviceClass and DeviceSubclass construct #2 (comment)
• Requested by: @daniellovell