Plugin Check: audit custom-table direct database findings

[chubes4]

Summary

Most remaining packaged Plugin Check warnings are direct database/custom-table findings. These need review so WordPress.org-facing code is either clearly prepared/cached or intentionally justified.

Evidence

Packaged Plugin Check artifact:
/Users/chubes/Developer/wp-codebox@issue-167-plugin-check/artifacts/data-machine-package-plugin-check/runtime-mpoc8s65-1j1z9w/files/plugin-check/data-machine.json

Counts:

• PluginCheck.Security.DirectDB.UnescapedDBParameter: 105
• WordPress.DB.DirectDatabaseQuery.DirectQuery: 22
• WordPress.DB.DirectDatabaseQuery.NoCaching: 22
• WordPress.DB.DirectDatabaseQuery.SchemaChange: 13

Top affected files:

• inc/Core/Database/Jobs/Jobs.php: 64 findings
• inc/Core/Database/ProcessedItems/ProcessedItems.php: 19 findings
• inc/Cli/Commands/ProcessedItemsCommand.php: 14 findings
• inc/Core/Database/Pipelines/Pipelines.php: 12 findings
• inc/Abilities/Job/RecoverStuckJobsAbility.php: 10 findings

Proposed fix

• Audit each custom-table query for correct $wpdb->prepare() usage and safe dynamic table/column handling.
• Add caching where appropriate or add narrowly scoped inline ignores with a clear explanation when a direct query is intentional and cache-inappropriate.
• Separate schema-change operations from runtime query paths where possible.

Acceptance criteria

• Packaged Plugin Check run has materially reduced custom-table/direct DB findings.
• Any remaining direct DB ignores are narrow, documented, and tied to intentional custom-table behavior.