reset upstream subtrees to yocto 2.6

Reset the following subtrees on thud HEAD:

  poky: 87e3a9739d
  meta-openembedded: 6094ae18c8
  meta-security: 31dc4e7532
  meta-raspberrypi: a48743dc36
  meta-xilinx: c42016e2e6

Also re-apply backports that didn't make it into thud:
  poky:
    17726d0 systemd-systemctl-native: handle Install wildcards

  meta-openembedded:
    4321a5d libtinyxml2: update to 7.0.1
    042f0a3 libcereal: Add native and nativesdk classes
    e23284f libcereal: Allow empty package
    030e8d4 rsyslog: curl-less build with fmhttp PACKAGECONFIG
    179a1b9 gtest: update to 1.8.1

Squashed OpenBMC subtree compatibility updates:
  meta-aspeed:
    Brad Bishop (1):
          aspeed: add yocto 2.6 compatibility

  meta-ibm:
    Brad Bishop (1):
          ibm: prepare for yocto 2.6

  meta-ingrasys:
    Brad Bishop (1):
          ingrasys: set layer compatibility to yocto 2.6

  meta-openpower:
    Brad Bishop (1):
          openpower: set layer compatibility to yocto 2.6

  meta-phosphor:
    Brad Bishop (3):
          phosphor: set layer compatibility to thud
          phosphor: libgpg-error: drop patches
          phosphor: react to fitimage artifact rename

    Ed Tanous (4):
          Dropbear: upgrade options for latest upgrade
          yocto2.6: update openssl options
          busybox: remove upstream watchdog patch
          systemd: Rebase CONFIG_CGROUP_BPF patch

Change-Id: I7b1fe71cca880d0372a82d94b5fd785323e3a9e7
Signed-off-by: Brad Bishop <bradleyb@fuzziesquirrel.com>
diff --git a/poky/meta/recipes-devtools/python/python3/create_manifest3.py b/poky/meta/recipes-devtools/python/python3/create_manifest3.py
index 2f944f9..fddb23c 100644
--- a/poky/meta/recipes-devtools/python/python3/create_manifest3.py
+++ b/poky/meta/recipes-devtools/python/python3/create_manifest3.py
@@ -43,194 +43,239 @@
 import subprocess
 import json
 import os
+import collections
+
+# Get python version from ${PYTHON_MAJMIN}
+pyversion = str(sys.argv[1])
 
 # Hack to get native python search path (for folders), not fond of it but it works for now
-pivot='recipe-sysroot-native'
+pivot = 'recipe-sysroot-native'
 for p in sys.path:
-  if pivot in p:
-    nativelibfolder=p[:p.find(pivot)+len(pivot)]
+    if pivot in p:
+        nativelibfolder = p[:p.find(pivot)+len(pivot)]
 
 # Empty dict to hold the whole manifest
-new_manifest = {}
+new_manifest = collections.OrderedDict()
 
 # Check for repeated files, folders and wildcards
-allfiles=[]
-repeated=[]
-wildcards=[]
+allfiles = []
+repeated = []
+wildcards = []
 
-hasfolders=[]
-allfolders=[]
+hasfolders = []
+allfolders = []
 
 def isFolder(value):
-  if os.path.isdir(value.replace('${libdir}',nativelibfolder+'/usr/lib')) or os.path.isdir(value.replace('${libdir}',nativelibfolder+'/usr/lib64')) or os.path.isdir(value.replace('${libdir}',nativelibfolder+'/usr/lib32')):
-    return True
-  else:
-    return False
+    value = value.replace('${PYTHON_MAJMIN}',pyversion)
+    if os.path.isdir(value.replace('${libdir}',nativelibfolder+'/usr/lib')) or os.path.isdir(value.replace('${libdir}',nativelibfolder+'/usr/lib64')) or os.path.isdir(value.replace('${libdir}',nativelibfolder+'/usr/lib32')):
+        return True
+    else:
+        return False
 
 def isCached(item):
-  if '__pycache__' in item:
-    return True
-  else:
-    return False
+    if '__pycache__' in item:
+        return True
+    else:
+        return False
 
 # Read existing JSON manifest
 with open('python3-manifest.json') as manifest:
-  old_manifest=json.load(manifest)
+    old_manifest = json.load(manifest, object_pairs_hook=collections.OrderedDict)
 
-
+#
 # First pass to get core-package functionality, because we base everything on the fact that core is actually working
 # Not exactly the same so it should not be a function
+#
+
 print ('Getting dependencies for package: core')
 
-# Special call to check for core package
+
+# This special call gets the core dependencies and
+# appends to the old manifest so it doesnt hurt what it
+# currently holds.
+# This way when other packages check for dependencies
+# on the new core package, they will still find them
+# even when checking the old_manifest
+
 output = subprocess.check_output([sys.executable, 'get_module_deps3.py', 'python-core-package']).decode('utf8')
-for item in output.split():
-    # We append it so it doesnt hurt what we currently have:
-    if isCached(item):
-        if item not in old_manifest['core']['cached']:
-            # We use the same data structure since its the one which will be used to check
-            # dependencies for other packages
-            old_manifest['core']['cached'].append(item)
+for coredep in output.split():
+    coredep = coredep.replace(pyversion,'${PYTHON_MAJMIN}')
+    if isCached(coredep):
+        if coredep not in old_manifest['core']['cached']:
+            old_manifest['core']['cached'].append(coredep)
     else:
-        if item not in old_manifest['core']['files']:
-            # We use the same data structure since its the one which will be used to check
-            # dependencies for other packages
-            old_manifest['core']['files'].append(item)
-
-for value in old_manifest['core']['files']:
-  # Ignore folders, since we don't import those, difficult to handle multilib
-  if isFolder(value):
-    # Pass it directly
-    if isCached(value):
-        if value not in old_manifest['core']['cached']:
-            old_manifest['core']['cached'].append(value)
-    else:
-        if value not in old_manifest['core']['files']:
-            old_manifest['core']['files'].append(value)
-    continue
-  # Ignore binaries, since we don't import those, assume it was added correctly (manually)
-  if '${bindir}' in value:
-    # Pass it directly
-    if value not in old_manifest['core']['files']:
-      old_manifest['core']['files'].append(value)
-    continue
-  # Ignore empty values
-  if value == '':
-    continue
-  if '${includedir}' in value:
-    if value not in old_manifest['core']['files']:
-      old_manifest['core']['files'].append(value)
-    continue
-  # Get module name , shouldnt be affected by libdir/bindir
-  value = os.path.splitext(os.path.basename(os.path.normpath(value)))[0]
-
-  # Launch separate task for each module for deterministic behavior
-  # Each module will only import what is necessary for it to work in specific
-  print ('Getting dependencies for module: %s' % value)
-  output = subprocess.check_output([sys.executable, 'get_module_deps3.py', '%s' % value]).decode('utf8')
-  print ('The following dependencies were found for module %s:\n' % value)
-  print (output)
-  for item in output.split():
-    # We append it so it doesnt hurt what we currently have:
-    if isCached(item):
-        if item not in old_manifest['core']['cached']:
-            # We use the same data structure since its the one which will be used to check
-            # dependencies for other packages
-            old_manifest['core']['cached'].append(item)
-    else:
-        if item not in old_manifest['core']['files']:
-            # We use the same data structure since its the one which will be used to check
-            # dependencies for other packages
-            old_manifest['core']['files'].append(item)
+        if coredep not in old_manifest['core']['files']:
+            old_manifest['core']['files'].append(coredep)
 
 
-# We check which packages include folders
-for key in old_manifest:
-    for value in old_manifest[key]['files']:
-        # Ignore folders, since we don't import those, difficult to handle multilib
-        if isFolder(value):
-            print ('%s is a folder' % value)
-            if key not in hasfolders:
-                hasfolders.append(key)
-            if value not in allfolders:
-                allfolders.append(value)
+# The second step is to loop through the existing files contained in the core package
+# according to the old manifest, identify if they are  modules, or some other type 
+# of file that we cant import (directories, binaries, configs) in which case we
+# can only assume they were added correctly (manually) so we ignore those and 
+# pass them to the manifest directly.
 
-for key in old_manifest:
+for filedep in old_manifest['core']['files']:
+    if isFolder(filedep):
+        if isCached(filedep):
+            if filedep not in old_manifest['core']['cached']:
+                old_manifest['core']['cached'].append(filedep)
+        else:
+            if filedep not in old_manifest['core']['files']:
+                old_manifest['core']['files'].append(filedep)
+        continue
+    if '${bindir}' in filedep:
+        if filedep not in old_manifest['core']['files']:
+            old_manifest['core']['files'].append(filedep)
+        continue
+    if filedep == '':
+        continue
+    if '${includedir}' in filedep:
+        if filedep not in old_manifest['core']['files']:
+            old_manifest['core']['files'].append(filedep)
+        continue
+
+    # Get actual module name , shouldnt be affected by libdir/bindir, etc.
+    pymodule = os.path.splitext(os.path.basename(os.path.normpath(filedep)))[0]
+
+
+    # We now know that were dealing with a python module, so we can import it
+    # and check what its dependencies are.
+    # We launch a separate task for each module for deterministic behavior.
+    # Each module will only import what is necessary for it to work in specific.
+    # The output of each task will contain each module's dependencies
+
+    print ('Getting dependencies for module: %s' % pymodule)
+    output = subprocess.check_output([sys.executable, 'get_module_deps3.py', '%s' % pymodule]).decode('utf8')
+    print ('The following dependencies were found for module %s:\n' % pymodule)
+    print (output)
+
+
+    for pymodule_dep in output.split():
+        pymodule_dep = pymodule_dep.replace(pyversion,'${PYTHON_MAJMIN}')
+
+        if isCached(pymodule_dep):
+            if pymodule_dep not in old_manifest['core']['cached']:
+                old_manifest['core']['cached'].append(pymodule_dep)
+        else:
+            if pymodule_dep not in old_manifest['core']['files']:
+                old_manifest['core']['files'].append(pymodule_dep)
+
+
+# At this point we are done with the core package.
+# The old_manifest dictionary is updated only for the core package because
+# all others will use this a base.
+
+
+# To improve the script speed, we check which packages contain directories
+# since we will be looping through (only) those later.
+for pypkg in old_manifest:
+    for filedep in old_manifest[pypkg]['files']:
+        if isFolder(filedep):
+            print ('%s is a folder' % filedep)
+            if pypkg not in hasfolders:
+                hasfolders.append(pypkg)
+            if filedep not in allfolders:
+                allfolders.append(filedep)
+
+
+
+# This is the main loop that will handle each package.
+# It works in a similar fashion than the step before, but
+# we will now be updating a new dictionary that will eventually
+# become the new manifest.
+#
+# The following loops though all packages in the manifest,
+# through all files on each of them, and checks whether or not
+# they are modules and can be imported.
+# If they can be imported, then it checks for dependencies for
+# each of them by launching a separate task.
+# The output of that task is then parsed and the manifest is updated
+# accordingly, wether it should add the module on FILES for the current package
+# or if that module already belongs to another package then the current one 
+# will RDEPEND on it
+
+for pypkg in old_manifest:
     # Use an empty dict as data structure to hold data for each package and fill it up
-    new_manifest[key]={}
-    new_manifest[key]['files']=[]
-    
-    new_manifest[key]['rdepends']=[]
+    new_manifest[pypkg] = collections.OrderedDict()
+    new_manifest[pypkg]['summary'] = old_manifest[pypkg]['summary']
+    new_manifest[pypkg]['rdepends'] = []
+    new_manifest[pypkg]['files'] = []
+    new_manifest[pypkg]['cached'] = old_manifest[pypkg]['cached']
+
     # All packages should depend on core
-    if key != 'core':
-         new_manifest[key]['rdepends'].append('core')
-         new_manifest[key]['cached']=[]
-    else:
-         new_manifest[key]['cached']=old_manifest[key]['cached']
-    new_manifest[key]['summary']=old_manifest[key]['summary']
+    if pypkg != 'core':
+        new_manifest[pypkg]['rdepends'].append('core')
+        new_manifest[pypkg]['cached'] = []
+
+    print('\n')
+    print('--------------------------')
+    print ('Handling package %s' % pypkg)
+    print('--------------------------')
 
     # Handle special cases, we assume that when they were manually added 
     # to the manifest we knew what we were doing.
-    print('\n')
-    print('--------------------------')
-    print ('Handling package %s' % key)
-    print('--------------------------')
-    special_packages=['misc', 'modules', 'dev']
-    if key in special_packages or 'staticdev' in key:
-        print('Passing %s package directly' % key)
-        new_manifest[key]=old_manifest[key]
+    special_packages = ['misc', 'modules', 'dev', 'tests']
+    if pypkg in special_packages or 'staticdev' in pypkg:
+        print('Passing %s package directly' % pypkg)
+        new_manifest[pypkg] = old_manifest[pypkg]
         continue
 
-    for value in old_manifest[key]['files']:
-        # We already handled core on the first pass
-        if key == 'core':
-            new_manifest[key]['files'].append(value)
-            continue
-        # Ignore folders, since we don't import those, difficult to handle multilib
-        if isFolder(value):
-            # Pass folders directly
-            new_manifest[key]['files'].append(value)
-        # Ignore binaries, since we don't import those
-        if '${bindir}' in value:
-            # Pass it directly to the new manifest data structure
-            if value not in new_manifest[key]['files']:
-                new_manifest[key]['files'].append(value)
-            continue
-        # Ignore empty values
-        if value == '':
-            continue
-        if '${includedir}' in value:
-            if value not in new_manifest[key]['files']:
-                new_manifest[key]['files'].append(value)
+    for filedep in old_manifest[pypkg]['files']:
+        # We already handled core on the first pass, we can ignore it now
+        if pypkg == 'core':
+            if filedep not in new_manifest[pypkg]['files']:
+                new_manifest[pypkg]['files'].append(filedep)
             continue
 
-        # Get module name , shouldnt be affected by libdir/bindir
+        # Handle/ignore what we cant import
+        if isFolder(filedep):
+            new_manifest[pypkg]['files'].append(filedep)
+            # Asyncio (and others) are both the package and the folder name, we should not skip those...
+            path,mod = os.path.split(filedep)
+            if mod != pypkg:
+                continue
+        if '${bindir}' in filedep:
+            if filedep not in new_manifest[pypkg]['files']:
+                new_manifest[pypkg]['files'].append(filedep)
+            continue
+        if filedep == '':
+            continue
+        if '${includedir}' in filedep:
+            if filedep not in new_manifest[pypkg]['files']:
+                new_manifest[pypkg]['files'].append(filedep)
+            continue
+
+        # Get actual module name , shouldnt be affected by libdir/bindir, etc.
         # We need to check if the imported module comes from another (e.g. sqlite3.dump)
-        path,value = os.path.split(value)
+        path,pymodule = os.path.split(filedep)
         path = os.path.basename(path)
-        value = os.path.splitext(os.path.basename(value))[0]
+        pymodule = os.path.splitext(os.path.basename(pymodule))[0]
 
         # If this condition is met, it means we need to import it from another module
         # or its the folder itself (e.g. unittest)
-        if path == key:
-          if value:
-            value = path + '.' + value
-          else:
-            value = path
+        if path == pypkg:
+            if pymodule:
+                pymodule = path + '.' + pymodule
+            else:
+                pymodule = path
 
-        # Launch separate task for each module for deterministic behavior
-        # Each module will only import what is necessary for it to work in specific
-        print ('\nGetting dependencies for module: %s' % value)
-        output = subprocess.check_output([sys.executable, 'get_module_deps3.py', '%s' % value]).decode('utf8')
-        # We can print dependencies for debugging purposes
-        print ('The following dependencies were found for module %s:\n' % value)
+
+
+        # We now know that were dealing with a python module, so we can import it
+        # and check what its dependencies are.
+        # We launch a separate task for each module for deterministic behavior.
+        # Each module will only import what is necessary for it to work in specific.
+        # The output of each task will contain each module's dependencies
+
+        print ('\nGetting dependencies for module: %s' % pymodule)
+        output = subprocess.check_output([sys.executable, 'get_module_deps3.py', '%s' % pymodule]).decode('utf8')
+        print ('The following dependencies were found for module %s:\n' % pymodule)
         print (output)
-        # Output will have all dependencies
 
         reportFILES = []
         reportRDEPS = []
 
-        for item in output.split():
+        for pymodule_dep in output.split():
 
             # Warning: This first part is ugly
             # One of the dependencies that was found, could be inside of one of the folders included by another package
@@ -250,22 +295,22 @@
             #   is folder_string inside path/folder1/folder2/filename?, 
             #   Yes, it works, but we waste a couple of milliseconds.
 
-            inFolders=False
+            pymodule_dep = pymodule_dep.replace(pyversion,'${PYTHON_MAJMIN}')
+            inFolders = False
             for folder in allfolders:
-                if folder in item:
+                if folder in pymodule_dep:
                     inFolders = True # Did we find a folder?
                     folderFound = False # Second flag to break inner for
                     # Loop only through packages which contain folders
-                    for keyfolder in hasfolders:
+                    for pypkg_with_folder in hasfolders:
                         if (folderFound == False):
-                            #print('Checking folder %s on package %s' % (item,keyfolder))
-                            for file_folder in old_manifest[keyfolder]['files'] or file_folder in old_manifest[keyfolder]['cached']:
-                                if file_folder==folder:
-                                    print ('%s folder found in %s' % (folder, keyfolder))
+                            # print('Checking folder %s on package %s' % (pymodule_dep,pypkg_with_folder))
+                            for folder_dep in old_manifest[pypkg_with_folder]['files'] or folder_dep in old_manifest[pypkg_with_folder]['cached']:
+                                if folder_dep == folder:
+                                    print ('%s folder found in %s' % (folder, pypkg_with_folder))
                                     folderFound = True
-                                    if keyfolder not in new_manifest[key]['rdepends'] and keyfolder != key:
-                                        new_manifest[key]['rdepends'].append(keyfolder)
-                                    
+                                    if pypkg_with_folder not in new_manifest[pypkg]['rdepends'] and pypkg_with_folder != pypkg:
+                                        new_manifest[pypkg]['rdepends'].append(pypkg_with_folder)
                         else:
                             break
 
@@ -274,81 +319,95 @@
                 continue
 
 
-            # We might already have it on the dictionary since it could depend on a (previously checked) module
-            if item not in new_manifest[key]['files'] and item not in new_manifest[key]['cached']:
+
+            # No directories beyond this point
+            # We might already have this module on the dictionary since it could depend on a (previously checked) module
+            if pymodule_dep not in new_manifest[pypkg]['files'] and pymodule_dep not in new_manifest[pypkg]['cached']:
                 # Handle core as a special package, we already did it so we pass it to NEW data structure directly
-                if key=='core':
-                  print('Adding %s to %s FILES' % (item, key))
-                  if item.endswith('*'):
-                      wildcards.append(item)
-                  if isCached(item):
-                      new_manifest[key]['cached'].append(item)
-                  else:
-                      new_manifest[key]['files'].append(item)
+                if pypkg == 'core':
+                    print('Adding %s to %s FILES' % (pymodule_dep, pypkg))
+                    if pymodule_dep.endswith('*'):
+                        wildcards.append(pymodule_dep)
+                    if isCached(pymodule_dep):
+                        new_manifest[pypkg]['cached'].append(pymodule_dep)
+                    else:
+                        new_manifest[pypkg]['files'].append(pymodule_dep)
 
-                  # Check for repeated files
-                  if item not in allfiles:
-                      allfiles.append(item)
-                  else:
-                      repeated.append(item)
-
+                    # Check for repeated files
+                    if pymodule_dep not in allfiles:
+                        allfiles.append(pymodule_dep)
+                    else:
+                        if pymodule_dep not in repeated:
+                            repeated.append(pymodule_dep)
                 else:
 
 
-                    # Check if this dependency is already contained on another package, so we add it
+                    # Last step: Figure out if we this belongs to FILES or RDEPENDS
+                    # We check if this module is already contained on another package, so we add that one
                     # as an RDEPENDS, or if its not, it means it should be contained on the current
-                    # package, so we should add it to FILES
-                    for newkey in old_manifest:
+                    # package, and we should add it to FILES
+                    for possible_rdep in old_manifest:
                         # Debug
-                        #print('Checking %s ' % item + ' in %s' % newkey)
-                        if item in old_manifest[newkey]['files'] or item in old_manifest[newkey]['cached']:      
-                                # Since were nesting, we need to check its not the same key
-                                if(newkey!=key):
-                                    if newkey not in new_manifest[key]['rdepends']:
-                                       # Add it to the new manifest data struct
-                                       reportRDEPS.append('Adding %s to %s RDEPENDS, because it contains %s\n' % (newkey, key, item))
-                                       new_manifest[key]['rdepends'].append(newkey)
-                                    break
+                        # print('Checking %s ' % pymodule_dep + ' in %s' % possible_rdep)
+                        if pymodule_dep in old_manifest[possible_rdep]['files'] or pymodule_dep in old_manifest[possible_rdep]['cached']:
+                            # Since were nesting, we need to check its not the same pypkg
+                            if(possible_rdep != pypkg):
+                                if possible_rdep not in new_manifest[pypkg]['rdepends']:
+                                    # Add it to the new manifest data struct as RDEPENDS since it contains something this module needs
+                                    reportRDEPS.append('Adding %s to %s RDEPENDS, because it contains %s\n' % (possible_rdep, pypkg, pymodule_dep))
+                                    new_manifest[pypkg]['rdepends'].append(possible_rdep)
+                                break
                     else:
-                      # A module shouldn't contain itself (${libdir}/python3/sqlite3 shouldnt be on sqlite3 files)
-                      if os.path.basename(item) != key:
-                        reportFILES.append(('Adding %s to %s FILES\n' % (item, key)))
-                        # Since it wasnt found on another package, its not an RDEP, so add it to FILES for this package
-                        if isCached(item):
-                            new_manifest[key]['cached'].append(item)
-                        else:
-                            new_manifest[key]['files'].append(item)
 
-                        if item.endswith('*'):
-                            wildcards.append(item)
-                        if item not in allfiles:
-                            allfiles.append(item)
+                      # Since this module wasnt found on another package, it is not an RDEP,
+                      # so we add it to FILES for this package.
+                      # A module shouldn't contain itself (${libdir}/python3/sqlite3 shouldnt be on sqlite3 files)
+                      if os.path.basename(pymodule_dep) != pypkg:
+                        reportFILES.append(('Adding %s to %s FILES\n' % (pymodule_dep, pypkg)))
+                        if isCached(pymodule_dep):
+                            new_manifest[pypkg]['cached'].append(pymodule_dep)
                         else:
-                            repeated.append(item)
+                            new_manifest[pypkg]['files'].append(pymodule_dep)
+                        if pymodule_dep.endswith('*'):
+                            wildcards.append(pymodule_dep)
+                        if pymodule_dep not in allfiles:
+                            allfiles.append(pymodule_dep)
+                        else:
+                            if pymodule_dep not in repeated:
+                                repeated.append(pymodule_dep)
 
         print('\n')
         print('#################################')
-        print('Summary for module %s' % value)
-        print('FILES found for module %s:' % value)
+        print('Summary for module %s' % pymodule)
+        print('FILES found for module %s:' % pymodule)
         print(''.join(reportFILES))
-        print('RDEPENDS found for module %s:' % value)
+        print('RDEPENDS found for module %s:' % pymodule)
         print(''.join(reportRDEPS))
         print('#################################')
 
-print ('The following files are repeated (contained in more than one package), please check which package should get it:')
-print (repeated)
-print('The following files contain wildcards, please check they are necessary')
+print('The following FILES contain wildcards, please check if they are necessary')
 print(wildcards)
-print('The following files contain folders, please check they are necessary')
+print('The following FILES contain folders, please check if they are necessary')
 print(hasfolders)
 
+
 # Sort it just so it looks nicer
-for key in new_manifest:
-    new_manifest[key]['files'].sort()
-    new_manifest[key]['cached'].sort()
-    new_manifest[key]['rdepends'].sort()
+for pypkg in new_manifest:
+    new_manifest[pypkg]['files'].sort()
+    new_manifest[pypkg]['cached'].sort()
+    new_manifest[pypkg]['rdepends'].sort()
 
 # Create the manifest from the data structure that was built
 with open('python3-manifest.json.new','w') as outfile:
-    json.dump(new_manifest,outfile,sort_keys=True, indent=4)
+    json.dump(new_manifest,outfile, indent=4)
     outfile.write('\n')
+
+if (repeated):
+    error_msg = '\n\nERROR:\n'
+    error_msg += 'The following files are repeated (contained in more than one package),\n'
+    error_msg += 'this is likely to happen when new files are introduced after an upgrade,\n'
+    error_msg += 'please check which package should get it,\n modify the manifest accordingly and re-run the create_manifest task:\n'
+    error_msg += '\n'.join(repeated)
+    error_msg += '\n'
+    sys.exit(error_msg)
+