Improve patch deduplication to avoid posting technically identical patches
### Problem/Motivation
Fix a bug where multiple projects would generate technically identical rector patches but post them independently, leading to duplicate comments. Isolate per-workspace SQLite databases by rewriting absolute paths to relative so drush si settings are not shared, reset workspace state between projects, and drop leftover database WAL/SHM files and container cache.
### Work items
- Commit(s): [86a03eacf2](https://git.drupalcode.org/project/project_analysis/-/commit/86a03eacf255), [579cd3c03a](https://git.drupalcode.org/project/project_analysis/-/commit/579cd3c03a71), [7057095ac9](https://git.drupalcode.org/project/project_analysis/-/commit/7057095ac947)
### Credit
- Implemented by: @bbrala
- Reported by: @guignonv
- Test-project feedback: @goba, @nicxvan, @wimleers, @rfay, @larowlan
---
*Filed retroactively as part of the Drupal 12 rector coverage effort. Closed as fixed; credit to be applied to the contributors listed above.*
*AI was used extensively to build this work and to file this issue. See [Dries Buytaert: AI-generated Rector rules for Drupal](https://dri.es/ai-generated-rector-rules-for-drupal) and [Björn Brala: Drupal Rector rules are config, not code. Mostly.](https://www.linkedin.com/pulse/drupal-rector-rules-config-code-mostly-bj%C3%B6rn-brala-vfpwe/).*
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