Resolve "Cannot delete and upload file of the same name in the Web IDE"

What does this MR do?

Resolves #60859 (closed).

In more details it changes some things in the way we handle entries when those get deleted in Web IDE:

• when an entry gets deleted, this change gets staged right away. This is per original git design: when running git rm MY_FILE git stages the delete right away exactly to allow for adding new files with the same name
• now we can add new entries to the same path
• when adding a new file of the same path as deleted one, it's marked with replaces: true but otherwise behaves as any other tempEntry and can be staged
• once this tempEntry gets staged, it replaces original entry on the same path. But before that, the original entry gets added to state.replacedFiles for easier discarding the changes later
• after tempEntry gets committed and hence replaces original entry in the repository, it gets replaces: false and state.replacedFiles gets emptied.

Does this MR meet the acceptance criteria?

Conformity

• Changelog entry
• 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