fix: CodeQL recommendations

[jay-dee7]

Motivation & Context:

In our mock FS implementations (File based and In-Memory based), we were not validating file input paths. CodeQL keeps on complaining about the paths, so now we just validate the paths before performing actions using file path inputs

Description:

• Validate paths ensuring they always start with layers.
• Also bumps the Bun ORM dependencies to latest

Types of Changes:

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

PR Checklist:

• My code follows the code style of this project
• My change requires a change to the documentation
• I have updated the documentation accordingly
• I've read the CONTRIBUTION guide
• I have signed-off my commits with git commit -s

[guacamole]

LGTM 🥇