Handle delayed or missed watches for project updates

[sheetalkamat]

This has two things:

• We invoke sourceFileChange when invoking wild card watcher to ensure fileExists status is updated. We do this because sometimes we only get "folder" added and deleted events and not actual file moved events.
• In our cached directory structure, earlier we were ignoring events for files/folders whose parent didnt have cached entries. but in cases where we are getting say event for "folder/functions/whatever" while creating "functions/whatever", we would not cleanup structure for "folder" and hence it would still assume "functions" does not exist in "folder". This fixes it.

This is kind of continuation of #59418 to deal with debounced watch events in a better way

Fixes repro reported in #59603 (comment)

[typescript-bot]

Looks like you're introducing a change to the public API surface area. If this includes breaking changes, please document them on our wiki's API Breaking Changes page.

Also, please make sure @DanielRosenwasser and @RyanCavanaugh are aware of the changes, just as a heads up.