Fix up pyo stale file handling

We were not doing what the comments said we should, and we also
want to change what happens in the case of an old py file from
a previous layer (such as a base layer in a runtime) has a non-rewritten
.pyc file. In that case we want to assume its correct and fix it up.

builder/builder-module.c

@@ -1078,8 +1078,8 @@ fixup_python_timestamp (int dfd,
            * pyc mtime == 1: (.pyc is from an old commited module)
            *     py mtime == 1: Do nothing, already correct
            *     py mtime != 1: The py changed in this module, remove pyc
-           * pyc mtime != 1: (.pyc changed this module)
-           *     py == 1: Shouldn't really happen, but for safety, remove pyc
+           * pyc mtime != 1: (.pyc changed this module, or was never rewritten in base layer)
+           *     py == 1: Shouldn't happen in flatpak-builder, but could be an un-rewritten ctime lower layer, assume it matches and update timestamp
            *     py mtime != pyc mtime: new pyc doesn't match last py written in this module, remove it
            *     py mtime == pyc mtime: These match, but the py will be set to mtime 1 by ostree, so update timestamp in pyc.
            */
@@ -1097,7 +1097,7 @@ fixup_python_timestamp (int dfd,
             }
           else /* pyc_mtime != 1 */
             {
-              if (pyc_mtime == stbuf.st_mtime || stbuf.st_mtime == 1)
+              if (pyc_mtime != stbuf.st_mtime && stbuf.st_mtime != 1)
                 remove_pyc = TRUE;
               /* else change mtime */
             }