#881 Extend/deprecate FileAppStream constructors

Cleanup FileAppStream usage.

• Start is quite straightforward.
• "CIF documentation plot generation" is not an app.framework app, didn't try to have an absolute path.
• "CIF simulator" internals are tricky.
• The app.framework CrashReport uses absolute paths
• Tooldef update is probably fine.

This patch has some cases where reported errors now print the user-supplied path. That hopefully doesn't cause trouble in changed output.

Addresses #881