rose app-run: file installation fixes.

1. Ensure executable sources results in executable an target.
2. Attempt to read large files no longer results in memory error.
   This is achieved by reading the file in blocks.
3. Don't bother to checksum directory contents if `mode=mkdir`.
Merge pull request #623 from matthewrmshin/fix.rose-app-run

rose app-run: file installation fixes.