store all patches in self.all_patches, use this for copying patches to repo/reprod

Author: bedroge

easybuild/framework/easyblock.py

@@ -188,6 +188,7 @@ def __init__(self, ec, logfile=None):
 
         # list of patch/source files, along with checksums
         self.patches = []
+        self.all_patches = [] # also includes patches of extensions
         self.src = []
         self.data_src = []
         self.checksums = []
@@ -601,6 +602,7 @@ def fetch_patches(self, patch_specs=None, extension=False, checksums=None):
                 patch_info['path'] = path
                 patch_info['checksum'] = self.get_checksum_for(checksums, filename=patch_info['name'], index=index)
 
+                self.all_patches.append(patch_info)
                 if extension:
                     patches.append(patch_info)
                 else:
@@ -5126,10 +5128,7 @@ def ensure_writable_log_dir(log_dir):
                     block = det_full_ec_version(app.cfg) + ".block"
                     repo.add_easyconfig(ecdict['original_spec'], app.name, block, buildstats, currentbuildstats)
                 repo.add_easyconfig(spec, app.name, det_full_ec_version(app.cfg), buildstats, currentbuildstats)
-                patches = app.patches
-                for ext in app.exts:
-                    patches += ext.get('patches', [])
-                for patch in patches:
+                for patch in app.all_patches:
                     if 'path' in patch:
                         repo.add_patch(patch['path'], app.name)
                 repo.commit("Built %s" % app.full_mod_name)
@@ -5153,10 +5152,7 @@ def ensure_writable_log_dir(log_dir):
                 _log.debug("Copied easyconfig file %s to %s", spec, newspec)
 
                 # copy patches
-                patches = app.patches
-                for ext in app.exts:
-                    patches += ext.get('patches', [])
-                for patch in patches:
+                for patch in app.all_patches:
                     if 'path' in patch:
                         target = os.path.join(new_log_dir, os.path.basename(patch['path']))
                         copy_file(patch['path'], target)