I have noticed a few odd things - maybe these are not officially supported - but seem they could potentially be fixed. This is with 0.48 I have noticed today.
If a rule is Always, and then modified to be any other type - it will continue to be applied as an always rule, even after clearing all chat’s. Only way to resolve is to clear and reindex whole project.
Reproduce - single rule in a repo to add a comment ‘foo’ to the top of every new file.
Always - works fine.
Change to manual - this should no longer apply, but foo still gets added.
Somewhat related - Auto select rules do not get loaded, pretty much never on their own, especially when a new file is created..
Same simple rule as above - but globs: *.ts (no description and auto set to false)
‘create a ts file to do xyz’ - file is created by agent (sonnet 3.5 or 3.7) - no foo at the top.
'add a function to file a.ts` - it MIGHT occasionally add foo to the existing file.