When using a stub make file based profile workflow as suggested in [Drush Make theory for happy profile development](https://www.drupal.org/node/1006620) I notice that patches to core are no longer applied.

I've tested this by reverting to a single make file workflow - core patches get applied just fine that way.

Has anyone else found a fix/workaround for this?

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UPDATE with details...

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Here's what my stub make file looks like:

    api = 2
    core = 7.x
    
    projects[] = drupal
    
    projects[example_profile][download][type] = "git"
    projects[example_profile][download][url] = "[email protected]:danohea/example-profile.git"
    projects[example_profile][type] = "profile"

Which as you can see is designed to go grab a custom profile. I should mention that that is not the real path to the profile (which is a private repo anyway).

The profile contains a further make file that looks a bit like this (shortened for convenience):

    api = 2
    core = 7.x
    
    ; Contrib modules (not in dev)
    
    ; Specify common subdir of "contrib"
    defaults[projects][subdir] = "contrib"
    
    projects[admin_menu][version] = 3
    projects[ctools][version] = 1
    projects[diff][version] = 3
    projects[eck][version] = 2
    projects[entity][version] = 1
    projects[jquery_update][version] = 3
    projects[libraries][version] = 2
    projects[link][version] = 1
    projects[module_filter][version] = 2
    projects[pathauto][version] = 1
    projects[token][version] = 1
    projects[transliteration][version] = 3
    projects[views][version] = 3
        
    ; Contrib modules (in dev)
    
    projects[wysiwyg][version] = 2.x-dev
    ; Keep in dev until this issue makes it to stable:
    ; https://drupal.org/node/1956778
        
    ; Themes
    
    projects[omega][version] = 4
    projects[omega][subdir] = "contrib"
    
    ; Libraries
    
    ; ckeditor
    libraries[ckeditor][download][type] = file
    libraries[ckeditor][download][url] = http://ckeditor.com/builder/download/a63002d0b001ab7841c8e29bb8081e57 
    
    ; Patches
    
    ; drupal
    ; Ignore front end vendor folders to improve directory search performance
    projects[drupal][patch][2329453] = https://www.drupal.org/files/issues/optimize_scan-2329453-84-do-not-test.patch
    
    ; pathauto
    ; Merge in pathauto_persist module functionality to prevent losing manual aliases with node_save() calls
    projects[pathauto][patch][936222] = https://www.drupal.org/files/issues/merge_in-936222-299.patch

The stub make file is run with a command that looks a bit like this:

    drush make --prepare-install path/to/stub.make -y

I'm running Drush version 7.0.0.

Note that there are 2 patches, one for drupal core and one for pathauto. The pathauto one is applied as expected, the drupal one doesn't seem to even run.

If I download & run the profile's make file directly (i.e. not via the stub) then the core patch is applied as expected.

If I move the drupal core patch to the stub make file, it still doesn't run.