Enable chat to operate on the most up to date information during edits

**Users report:**
> I had bypassed Q to fix something, it kept trying to undo my fixes [on subsequent edits].

**Explanation:**
Q CLI is not aware of the context associated with the change in file made since its last edit.
As such, subsequent edits initiated by the model will try to revert said changes as to establish continuity with the context it does have.

**Goal:**
- Changes made by the users should be respected by the model on subsequent model initiated edits

No file, test, or entry point is named. Start by tracing how Q CLI tracks file changes between model-initiated edits; done means subsequent edits respect changes made by the user instead of reverting them.

Written by the indexing model from the issue text.