chat: fix file recreation after deletion (#289986)

Fixes a bug where if a file is deleted and the agent then tries to
recreate it again (by doing an edit in startStreamingEdits) nothing
happens.

- If there is an existing deleted entry for the file and it has NOT been
  accepted, then replace it with the correct modified file entry. Takes
  the originalContent of the deleted file as the initial content of the
  new file.
- If the deleted entry HAS been accepted (is not in the modified state)
  then it is just discarded and replaced.

Fixes https://github.com/microsoft/vscode/issues/289925

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