Fixed deletion of directories in Web IDE

What does this MR do?

Precisely follows proposal in #64677 (closed):

• when simply emptying a folder, the behavior isn't changed: the folder remains in the tree unless browser window reloaded
• when the whole folder is removed, the folder is filtered out from the data sent to Commit API to avoid failed request. The folder is removed from the tree view as well in this case.

Does this MR meet the acceptance criteria?

Conformity

• Changelog entry for user-facing changes, or community contribution. Check the link for other scenarios.
• Documentation created/updated or follow-up review issue created
• Code review guidelines
• Merge request performance guidelines
• Style guides
• Database guides
• Separation of EE specific content

Performance and Testing

• Review and add/update tests for this feature/bug. Consider all test levels. See the Test Planning Process.
• Tested in all supported browsers

Closes #64677 (closed)