Fix dirty flag

Git diff-index doesn't rebuild index, so files with modified dates or touched
are marked as modified with a SHA1 of all 0.

To fix this, we run update-index --refresh before diff index. Any touched
files are updated in the index.

https://stackoverflow.com/questions/36367190/git-diff-files-output-changes-after-git-status

old-commit-hash: 0a7fed9437

selfdrive/version.py

@@ -13,6 +13,7 @@ try:
     else:
       branch = subprocess.check_output(["git", "rev-parse", "--abbrev-ref", "HEAD"]).rstrip()
       branch = 'origin/' + branch
+      subprocess.check_call(["git", "update-index", "--refresh"])  #This is needed otherwise touched files might show up as modified
       dirty = subprocess.call(["git", "diff-index", "--quiet", branch, "--"]) != 0
       if dirty:
         dirty_files = subprocess.check_output(["git", "diff-index", branch, "--"])