bitbake-layers: flatten improvements

index b2781bb..572487d 100755
@@ -139,9 +139,10 @@ Highest priority recipes are listed with the recipes they overlay as subitems.
     def do_flatten(self, args):
         """flattens layer configuration into a separate output directory.
 
-usage: flatten <outputdir>
+usage: flatten [layer1 layer2 [layer3]...] <outputdir>
 
-Takes the current layer configuration and builds a "flattened" directory
+Takes the specified layers (or all layers in the current layer
+configuration if none are specified) and builds a "flattened" directory
 containing the contents of all layers, with any overlayed recipes removed
 and bbappends appended to the corresponding recipes. Note that some manual
 cleanup may still be necessary afterwards, in particular:

@@ -149,21 +150,59 @@ cleanup may still be necessary afterwards, in particular:
 * where non-recipe files (such as patches) are overwritten (the flatten
   command will show a warning for these)
 * where anything beyond the normal layer setup has been added to
-  layer.conf (only the lowest priority layer's layer.conf is used)
+  layer.conf (only the lowest priority number layer's layer.conf is used)
 * overridden/appended items from bbappends will need to be tidied up
+
+Warning: if you flatten several layers where another layer is intended to
+be used "inbetween" them (in layer priority order) such that recipes /
+bbappends in the layers interact, and then attempt to use the new output
+layer together with that other layer, you may no longer get the same
+build results (as the layer priority order has effectively changed).
 """
         arglist = args.split()
-        if len(arglist) != 1:
+        if len(arglist) < 1:
             logger.error('Please specify an output directory')
             self.do_help('flatten')
             return
 
-        if os.path.exists(arglist[0]) and os.listdir(arglist[0]):
-            logger.error('Directory %s exists and is non-empty, please clear it out first' % arglist[0])
+        if len(arglist) == 2:
+            logger.error('If you specify layers to flatten you must specify at least two')
+            self.do_help('flatten')
+            return
+
+        outputdir = arglist[-1]
+        if os.path.exists(outputdir) and os.listdir(outputdir):
+            logger.error('Directory %s exists and is non-empty, please clear it out first' % outputdir)
             return
 
         self.check_prepare_cooker()
         layers = (self.config_data.getVar('BBLAYERS', True) or "").split()
+        if len(arglist) > 2:
+            layernames = arglist[:-1]
+            found_layernames = []
+            found_layerdirs = []
+            for layerdir in layers:
+                for layername, _, regex, _ in self.cooker.status.bbfile_config_priorities:
+                    if layername in layernames:
+                        if regex.match(os.path.join(layerdir, 'test')):
+                            found_layerdirs.append(layerdir)
+                            found_layernames.append(layername)
+                            break
+
+            for layername in layernames:
+                if not layername in found_layernames:
+                    logger.error('Unable to find layer %s in current configuration, please run "%s show_layers" to list configured layers' % (layername, os.path.basename(sys.argv[0])))
+                    return
+            layers = found_layerdirs
+
+        # Ensure a specified path matches our list of layers
+        def layer_path_match(path):
+            for layerdir in layers:
+                if path.startswith(os.path.join(layerdir, '')):
+                    return layerdir
+            return None
+
+        appended_recipes = []
         for layer in layers:
             overlayed = []
             for f in self.cooker.overlayed.iterkeys():

@@ -181,7 +220,7 @@ cleanup may still be necessary afterwards, in particular:
                         ext = os.path.splitext(f1)[1]
                         if ext != '.bbappend':
                             fdest = f1full[len(layer):]
-                            fdest = os.path.normpath(os.sep.join([arglist[0],fdest]))
+                            fdest = os.path.normpath(os.sep.join([outputdir,fdest]))
                             bb.utils.mkdirhier(os.path.dirname(fdest))
                             if os.path.exists(fdest):
                                 if f1 == 'layer.conf' and root.endswith('/conf'):

@@ -196,7 +235,27 @@ cleanup may still be necessary afterwards, in particular:
                                     if appends:
                                         logger.plain('  Applying appends to %s' % fdest )
                                         for appendname in appends:
-                                            self.apply_append(appendname, fdest)
+                                            if layer_path_match(appendname):
+                                                self.apply_append(appendname, fdest)
+                                    appended_recipes.append(f1)
+
+        # Take care of when some layers are excluded and yet we have included bbappends for those recipes
+        for recipename in self.cooker_data.appends.iterkeys():
+            if recipename not in appended_recipes:
+                appends = self.cooker_data.appends[recipename]
+                first_append = None
+                for appendname in appends:
+                    layer = layer_path_match(appendname)
+                    if layer:
+                        if first_append:
+                            self.apply_append(appendname, first_append)
+                        else:
+                            fdest = appendname[len(layer):]
+                            fdest = os.path.normpath(os.sep.join([outputdir,fdest]))
+                            bb.utils.mkdirhier(os.path.dirname(fdest))
+                            bb.utils.copyfile(appendname, fdest)
+                            first_append = fdest
+
 
     def get_append_layer(self, appendname):
         for layer, _, regex, _ in self.cooker.status.bbfile_config_priorities:

index 572487d..b4c4127 100755
@@ -8,6 +8,7 @@ import cmd
 import logging
 import os
 import sys
+import fnmatch
 
 bindir = os.path.dirname(__file__)
 topdir = os.path.dirname(bindir)

@@ -152,6 +153,8 @@ cleanup may still be necessary afterwards, in particular:
 * where anything beyond the normal layer setup has been added to
   layer.conf (only the lowest priority number layer's layer.conf is used)
 * overridden/appended items from bbappends will need to be tidied up
+* when the flattened layers do not have the same directory structure (the
+  flatten command should show a warning when this will cause a problem)
 
 Warning: if you flatten several layers where another layer is intended to
 be used "inbetween" them (in layer priority order) such that recipes /

@@ -194,6 +197,8 @@ build results (as the layer priority order has effectively changed).
                     logger.error('Unable to find layer %s in current configuration, please run "%s show_layers" to list configured layers' % (layername, os.path.basename(sys.argv[0])))
                     return
             layers = found_layerdirs
+        else:
+            layernames = []
 
         # Ensure a specified path matches our list of layers
         def layer_path_match(path):

@@ -256,6 +261,39 @@ build results (as the layer priority order has effectively changed).
                             bb.utils.copyfile(appendname, fdest)
                             first_append = fdest
 
+        # Get the regex for the first layer in our list (which is where the conf/layer.conf file will
+        # have come from)
+        first_regex = None
+        layerdir = layers[0]
+        for layername, pattern, regex, _ in self.cooker.status.bbfile_config_priorities:
+            if (not layernames) or layername in layernames:
+                if regex.match(os.path.join(layerdir, 'test')):
+                    first_regex = regex
+                    break
+
+        if first_regex:
+            # Find the BBFILES entries that match (which will have come from this conf/layer.conf file)
+            bbfiles = str(self.config_data.getVar('BBFILES', True)).split()
+            bbfiles_layer = []
+            for item in bbfiles:
+                if first_regex.match(item):
+                    newpath = os.path.join(outputdir, item[len(layerdir)+1:])
+                    bbfiles_layer.append(newpath)
+
+            if bbfiles_layer:
+                # Check that all important layer files match BBFILES
+                for root, dirs, files in os.walk(outputdir):
+                    for f1 in files:
+                        ext = os.path.splitext(f1)[1]
+                        if ext in ['.bb', '.bbappend']:
+                            f1full = os.sep.join([root, f1])
+                            entry_found = False
+                            for item in bbfiles_layer:
+                                if fnmatch.fnmatch(f1full, item):
+                                    entry_found = True
+                                    break
+                            if not entry_found:
+                                logger.warning("File %s does not match the flattened layer's BBFILES setting, you may need to edit conf/layer.conf or move the file elsewhere" % f1full)
 
     def get_append_layer(self, appendname):
         for layer, _, regex, _ in self.cooker.status.bbfile_config_priorities:

index b4c4127..b4cfd55 100755
@@ -307,6 +307,8 @@ build results (as the layer priority order has effectively changed).
         recipefile.write('\n')
         recipefile.write('##### bbappended from %s #####\n' % self.get_append_layer(appendname))
         recipefile.writelines(appendfile.readlines())
+        recipefile.close()
+        appendfile.close()
 
     def do_show_appends(self, args):
         """list bbappend files and recipe files they apply to