Support fixers which must look at files on disk

Some tools for fixing files might have to only work with files on disk in exactly the right path. ALE should support these tools. Here is what needs to be done.

1. Add a new option `fix_file` which when set to `1` will tell ALE that the file will be modified.
2. Before jobs for fixers with `fix_file` are run, write changes to the file so far with `writefile`.
3. After job for fixers with `fix_file` are finished, load the lines of input for the next fixer back from the file.
4. Fixers with `fix_file` set to `1` should be skipped when fixing is done from an event for fixing files while typing.