diff --git a/poky/scripts/lib/devtool/standard.py b/poky/scripts/lib/devtool/standard.py
index e3b74ab..d64e18e 100644
--- a/poky/scripts/lib/devtool/standard.py
+++ b/poky/scripts/lib/devtool/standard.py
@@ -765,6 +765,16 @@
         staging_kbranch = "".join(branch.split('\n')[0])
     return staging_kbranch
 
+def get_real_srctree(srctree, s, workdir):
+    # Check that recipe isn't using a shared workdir
+    s = os.path.abspath(s)
+    workdir = os.path.abspath(workdir)
+    if s.startswith(workdir) and s != workdir and os.path.dirname(s) != workdir:
+        # Handle if S is set to a subdirectory of the source
+        srcsubdir = os.path.relpath(s, workdir).split(os.sep, 1)[1]
+        srctree = os.path.join(srctree, srcsubdir)
+    return srctree
+
 def modify(args, config, basepath, workspace):
     """Entry point for the devtool 'modify' subcommand"""
     import bb
@@ -923,14 +933,7 @@
 
         # Need to grab this here in case the source is within a subdirectory
         srctreebase = srctree
-
-        # Check that recipe isn't using a shared workdir
-        s = os.path.abspath(rd.getVar('S'))
-        workdir = os.path.abspath(rd.getVar('WORKDIR'))
-        if s.startswith(workdir) and s != workdir and os.path.dirname(s) != workdir:
-            # Handle if S is set to a subdirectory of the source
-            srcsubdir = os.path.relpath(s, workdir).split(os.sep, 1)[1]
-            srctree = os.path.join(srctree, srcsubdir)
+        srctree = get_real_srctree(srctree, rd.getVar('S'), rd.getVar('WORKDIR'))
 
         bb.utils.mkdirhier(os.path.dirname(appendfile))
         with open(appendfile, 'w') as f:
@@ -1406,6 +1409,18 @@
     updated = OrderedDict()
     added = OrderedDict()
     removed = OrderedDict()
+
+    # Get current branch and return early with empty lists
+    # if on one of the override branches
+    # (local files are provided only for the main branch and processing
+    # them against lists from recipe overrides will result in mismatches
+    # and broken modifications to recipes).
+    stdout, _ = bb.process.run('git rev-parse --abbrev-ref HEAD',
+                               cwd=srctree)
+    branchname = stdout.rstrip()
+    if branchname.startswith(override_branch_prefix):
+        return (updated, added, removed)
+
     local_files_dir = os.path.join(srctreebase, 'oe-local-files')
     git_files = _git_ls_tree(srctree)
     if 'oe-local-files' in git_files:
@@ -1635,31 +1650,25 @@
     tempdir = tempfile.mkdtemp(prefix='devtool')
     try:
         local_files_dir = tempfile.mkdtemp(dir=tempdir)
-        if filter_patches:
-            upd_f = {}
-            new_f = {}
-            del_f = {}
-        else:
-            upd_f, new_f, del_f = _export_local_files(srctree, rd, local_files_dir, srctreebase)
-
-        remove_files = []
-        if not no_remove:
-            # Get all patches from source tree and check if any should be removed
-            all_patches_dir = tempfile.mkdtemp(dir=tempdir)
-            _, _, del_p = _export_patches(srctree, rd, initial_rev,
-                                          all_patches_dir)
-            # Remove deleted local files and  patches
-            remove_files = list(del_f.values()) + list(del_p.values())
+        upd_f, new_f, del_f = _export_local_files(srctree, rd, local_files_dir, srctreebase)
 
         # Get updated patches from source tree
         patches_dir = tempfile.mkdtemp(dir=tempdir)
         upd_p, new_p, _ = _export_patches(srctree, rd, update_rev,
                                           patches_dir, changed_revs)
+        # Get all patches from source tree and check if any should be removed
+        all_patches_dir = tempfile.mkdtemp(dir=tempdir)
+        _, _, del_p = _export_patches(srctree, rd, initial_rev,
+                                      all_patches_dir)
         logger.debug('Pre-filtering: update: %s, new: %s' % (dict(upd_p), dict(new_p)))
         if filter_patches:
             new_p = OrderedDict()
             upd_p = OrderedDict((k,v) for k,v in upd_p.items() if k in filter_patches)
-            remove_files = [f for f in remove_files if f in filter_patches]
+            del_p = OrderedDict((k,v) for k,v in del_p.items() if k in filter_patches)
+        remove_files = []
+        if not no_remove:
+            # Remove deleted local files and  patches
+            remove_files = list(del_f.values()) + list(del_p.values())
         updatefiles = False
         updaterecipe = False
         destpath = None
diff --git a/poky/scripts/lib/devtool/upgrade.py b/poky/scripts/lib/devtool/upgrade.py
index 39a1910..967d157 100644
--- a/poky/scripts/lib/devtool/upgrade.py
+++ b/poky/scripts/lib/devtool/upgrade.py
@@ -88,7 +88,7 @@
     _rename_recipe_dirs(oldpv, newpv, path)
     return _rename_recipe_file(oldrecipe, bpn, oldpv, newpv, path)
 
-def _write_append(rc, srctree, same_dir, no_same_dir, rev, copied, workspace, d):
+def _write_append(rc, srctreebase, srctree, same_dir, no_same_dir, rev, copied, workspace, d):
     """Writes an append file"""
     if not os.path.exists(rc):
         raise DevtoolError("bbappend not created because %s does not exist" % rc)
@@ -104,6 +104,11 @@
     af = os.path.join(appendpath, '%s.bbappend' % brf)
     with open(af, 'w') as f:
         f.write('FILESEXTRAPATHS:prepend := "${THISDIR}/${PN}:"\n\n')
+        # Local files can be modified/tracked in separate subdir under srctree
+        # Mostly useful for packages with S != WORKDIR
+        f.write('FILESPATH:prepend := "%s:"\n' %
+                os.path.join(srctreebase, 'oe-local-files'))
+        f.write('# srctreebase: %s\n' % srctreebase)
         f.write('inherit externalsrc\n')
         f.write(('# NOTE: We use pn- overrides here to avoid affecting'
                  'multiple variants in the case where the recipe uses BBCLASSEXTEND\n'))
@@ -524,14 +529,7 @@
         else:
             srctree = standard.get_default_srctree(config, pn)
 
-        # Check that recipe isn't using a shared workdir
-        s = os.path.abspath(rd.getVar('S'))
-        workdir = os.path.abspath(rd.getVar('WORKDIR'))
-        srctree_s = srctree
-        if s.startswith(workdir) and s != workdir and os.path.dirname(s) != workdir:
-            # Handle if S is set to a subdirectory of the source
-            srcsubdir = os.path.relpath(s, workdir).split(os.sep, 1)[1]
-            srctree_s = os.path.join(srctree, srcsubdir)
+        srctree_s = standard.get_real_srctree(srctree, rd.getVar('S'), rd.getVar('WORKDIR'))
 
         # try to automatically discover latest version and revision if not provided on command line
         if not args.version and not args.srcrev:
@@ -575,7 +573,7 @@
             _upgrade_error(e, recipedir, srctree, args.keep_failure)
         standard._add_md5(config, pn, os.path.dirname(rf))
 
-        af = _write_append(rf, srctree_s, args.same_dir, args.no_same_dir, rev2,
+        af = _write_append(rf, srctree, srctree_s, args.same_dir, args.no_same_dir, rev2,
                         copied, config.workspace_path, rd)
         standard._add_md5(config, pn, af)