Files need to be resaved on update

Seems to make sense - Moshe, you committed the lines in question, any thoughts?

Thanks.

Committed suggested fix to 7.x-2.x. Looks right to me. I think I was trying to save cycles but I miunderstood that file_save() is not part of file api but rather entity api.

I'm guessing you're not running into a Migrate bug. The URI field has a unique key but it's not case sensitive so if you have "public://foo" and "public://Foo" that'll throw the exception. See #966210: DB Case Sensitivity: system_update_7061() fails on inserting files with same name but different case for more.

Something else is wrong with the code in MigrateDestinationFile::import() for file saving.

<?php
    if (!file_load_multiple(array(), array('uri' => $file->uri))) {
?>

$file->uri is NOT the primary key for files!
The primary key is $file->fid.

Effect:
The migration will create new files, instead of updating existing ones.
In some cases this might not matter, but it does matter if you create stub files (such as, for user avatars).

The following things have to be checked:
- Is the $file->fid set, or are we creating a new file?
- If $file->fid is set, does this file actually exist?
- Does another file exist with the same filepath (uri)? Is this our friend that has the same fid, or is this something else?
- If $file->fid is set, and the file entity with that fid does exist already, do we have a modified uri?

So, here is the logic we should be using:

<?php
    // Look for existing files
    $existing_by_uri = file_load_multiple(array(), array('uri' => $file->uri));
    // TODO:
    //   We already load $old_file above, but only for Migration::DESTINATION.
    $old_file = file_load($file->fid);
    if (empty($file->fid)) {
      // We are creating a new file entity.
      if (!empty$existing_by_uri)) {
        // Another file entity does already exist, which refers to the same physical file.
        // -> dedupe the uri!
        // In fact, we should have done this before already.
        // So, we rather throw an exception.
        throw new MigrateException(t('Trying to create a new file entity for an already-existing physical file location.'));
      }
      else {
        // We are safe to create a new file.
        .. // create
      }
    }
    elseif (empty($old_file)) {
      // Trying to save a file with explicit fid,
      // but there is no existing entity to overwrite.
      // Do we allow this?
    }
    elseif {
      // This is an update.
      if ($old_file->uri === $file->uri) {
        // uri has not changed, but the file contents might have.
        // At least, we don't need to be afraid of conflicts with other file entities.
      }
      elseif (!empty($existing_by_uri)) {
        // Another file entity does already exist, with the same file location (uri).
        // -> dedupe the uri!
        // In fact, we should have done this before already.
        // So, we rather throw an exception.
        throw new MigrateException(t('Trying to update a file entity with an uri that is already occupied.'));
      }
      else {
        // uri has changed. file contents might have changed.
        // Delete the old one, create the new file, update the uri.
      }
    }
?>

Or am I missing something?

Amazing, now this does actually work :)

Here is a very basic patch.

EDIT:
There is probably a lot of redundancy with other parts of code, where things are already being checked.

Also, the dedupe stuff that I talk about in the comments, needs to happen somewhere. This all depends how the $file objects are prefilled with uri etc, stuff that is happening before this function.
Honestly, I did not study any of this.

Btw, about dedupe, there is also this beast still lurking.
#1358318: dedupe() overdedupes on --update
(for anyone who tries to work on this, this will be useful to know)

All this stuff about URIs has nothing to do with the original issue, it should be opened as a separate issue.

Damn, now I don't remember any of this.
Issue: #1400284: Offer options on how to handle uri collisions

I could wait for a better time to post this, but there is also the chance that I will totally drop it. So I rather do it now.