combo-layer enhancements

index 851003d..71fa7b127 100755
@@ -109,7 +109,9 @@ class Configuration(object):
                         readsection(self.localparser, section, repo)
 
     def update(self, repo, option, value, initmode=False):
-        if self.localparser:
+        # If the main config has the option already, that is what we
+        # are expected to modify.
+        if self.localparser and not self.parser.has_option(repo, option):
             parser = self.localparser
             section = "%s|%s" % (repo, self.combobranch)
             conffile = self.localconffile

index 71fa7b127..62f2cf8 100755
@@ -68,6 +68,11 @@ class Configuration(object):
                 if value.startswith("@"):
                     self.repos[repo][name] = eval(value.strip("@"))
                 else:
+                    # Apply special type transformations for some properties.
+                    # Type matches the RawConfigParser.get*() methods.
+                    types = {'signoff': 'boolean'}
+                    if name in types:
+                        value = getattr(parser, 'get' + types[name])(section, name)
                     self.repos[repo][name] = value
 
         logger.debug("Loading config file %s" % self.conffile)

@@ -482,7 +487,7 @@ def apply_patchlist(conf, repos):
                 if os.path.getsize(patchfile) == 0:
                     logger.info("(skipping %d/%d %s - no changes)" % (i, linecount, patchdisp))
                 else:
-                    cmd = "git am --keep-cr -s -p1 %s" % patchfile
+                    cmd = "git am --keep-cr %s-p1 %s" % ('-s ' if repo.get('signoff', True) else '', patchfile)
                     logger.info("Applying %d/%d: %s" % (i, linecount, patchdisp))
                     try:
                         runcmd(cmd)

index 010a692..427c1b3 100644
@@ -1,7 +1,17 @@
 # combo-layer example configuration file
 
+# Default values for all sections.
+[DEFAULT]
+
+# Add 'Signed-off-by' to all commits that get imported automatically.
+signoff = True
+
 # component name
 [bitbake]
+
+# Override signedoff default above (not very useful, but possible).
+signoff = False
+
 # mandatory options
 # git upstream uri
 src_uri = git://git.openembedded.org/bitbake

index 62f2cf8..3ee9eb2 100755
@@ -152,23 +152,27 @@ class Configuration(object):
             logger.error("ERROR: patchutils package is missing, please install it (e.g. # apt-get install patchutils)")
             sys.exit(1)
 
-def runcmd(cmd,destdir=None,printerr=True):
+def runcmd(cmd,destdir=None,printerr=True,out=None):
     """
         execute command, raise CalledProcessError if fail
         return output if succeed
     """
     logger.debug("run cmd '%s' in %s" % (cmd, os.getcwd() if destdir is None else destdir))
-    out = os.tmpfile()
+    if not out:
+        out = os.tmpfile()
+        err = out
+    else:
+        err = os.tmpfile()
     try:
-        subprocess.check_call(cmd, stdout=out, stderr=out, cwd=destdir, shell=True)
+        subprocess.check_call(cmd, stdout=out, stderr=err, cwd=destdir, shell=isinstance(cmd, str))
     except subprocess.CalledProcessError,e:
-        out.seek(0)
+        err.seek(0)
         if printerr:
-            logger.error("%s" % out.read())
+            logger.error("%s" % err.read())
         raise e
 
-    out.seek(0)
-    output = out.read()
+    err.seek(0)
+    output = err.read()
     logger.debug("output: %s" % output )
     return output
 

index 3ee9eb2..8db5d7e 100755
@@ -20,6 +20,7 @@
 # with this program; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 
+import fnmatch
 import os, sys
 import optparse
 import logging

@@ -211,7 +212,18 @@ def action_init(conf, args):
             else:
                 extract_dir = os.getcwd()
             file_filter = repo.get('file_filter', "")
-            runcmd("git archive %s | tar -x -C %s %s" % (initialrev, extract_dir, file_filter), ldir)
+            files = runcmd("git archive %s | tar -x -v -C %s %s" % (initialrev, extract_dir, file_filter), ldir)
+            exclude_patterns = repo.get('file_exclude', '').split()
+            if exclude_patterns:
+                # Implement file removal by letting tar create the
+                # file and then deleting it in the file system
+                # again. Uses the list of files created by tar (easier
+                # than walking the tree).
+                for file in files.split('\n'):
+                    for pattern in exclude_patterns:
+                        if fnmatch.fnmatch(file, pattern):
+                            os.unlink(os.path.join(extract_dir, file))
+                            break
             if not lastrev:
                 lastrev = runcmd("git rev-parse %s" % initialrev, ldir).strip()
                 conf.update(name, "last_revision", lastrev, initmode=True)

@@ -426,6 +438,34 @@ def action_update(conf, args):
                 runcmd("%s %s %s %s" % (repo['hook'], patch, revlist[count], name))
                 count=count-1
 
+        # Step 3a: Filter out unwanted files and patches.
+        exclude = repo.get('file_exclude', '')
+        if exclude:
+            filter = ['filterdiff', '-p1']
+            for path in exclude.split():
+                filter.append('-x')
+                filter.append('%s/%s' % (dest_dir, path) if dest_dir else path)
+            for patch in patchlist[:]:
+                filtered = patch + '.tmp'
+                with open(filtered, 'w') as f:
+                    runcmd(filter + [patch], out=f)
+                # Now check for empty patches.
+                if runcmd(['filterdiff', '--list', filtered]):
+                    # Possibly modified.
+                    os.unlink(patch)
+                    os.rename(filtered, patch)
+                else:
+                    # Empty, ignore it. Must also remove from revlist.
+                    with open(patch, 'r') as f:
+                        fromline = f.readline()
+                    m = re.match(r'''^From ([0-9a-fA-F]+) .*\n''', fromline)
+                    rev = m.group(1)
+                    logger.debug('skipping empty patch %s = %s' % (patch, rev))
+                    os.unlink(patch)
+                    os.unlink(filtered)
+                    patchlist.remove(patch)
+                    revlist.remove(rev)
+
         # Step 4: write patch list and revision list to file, for user to edit later
         patchlist_file = os.path.join(os.getcwd(), patch_dir, "patchlist-%s" % name)
         repo['patchlist'] = patchlist_file

index 427c1b3..38bc53c 100644
@@ -42,6 +42,20 @@ last_revision =
 #   file_filter = src/*.c : only include the src *.c file
 #   file_filter = src/main.c src/Makefile.am : only include these two files
 
+# file_exclude: filter out these file(s)
+# file_exclude = [path] [path] ...
+#
+# Each entry must match a file name. In contrast do file_filter, matching
+# a directory has no effect. To achieve that, use append a * wildcard
+# at the end.
+#
+# Wildcards are applied to the complete path and also match slashes.
+#
+# example:
+#   file_exclude = src/foobar/*  : exclude everything under src/foobar
+#   file_exclude = src/main.c : filter out main.c after including it with file_filter = src/*.c
+#   file_exclude = *~ : exclude backup files
+
 # hook: if provided, the tool will call the hook to process the generated
 #     patch from upstream, and then apply the modified patch to the combo
 #     repo.

index 8db5d7e..8ed9be8 100755
@@ -130,6 +130,7 @@ class Configuration(object):
         parser.set(section, option, value)
         with open(conffile, "w") as f:
             parser.write(f)
+        self.repos[repo][option] = value
 
     def sanity_check(self, initmode=False):
         required_options=["src_uri", "local_repo_dir", "dest_dir", "last_revision"]

index 8ed9be8..d11274e 100755
@@ -25,6 +25,7 @@ import os, sys
 import optparse
 import logging
 import subprocess
+import tempfile
 import ConfigParser
 import re
 from collections import OrderedDict

@@ -190,6 +191,11 @@ def action_init(conf, args):
             subprocess.check_call("git clone %s %s" % (conf.repos[name]['src_uri'], ldir), shell=True)
     if not os.path.exists(".git"):
         runcmd("git init")
+        if conf.history:
+            # Need a common ref for all trees.
+            runcmd('git commit -m "initial empty commit" --allow-empty')
+            startrev = runcmd('git rev-parse master').strip()
+
         for name in conf.repos:
             repo = conf.repos[name]
             ldir = repo['local_repo_dir']

@@ -205,6 +211,25 @@ def action_init(conf, args):
                 lastrev = None
                 initialrev = branch
                 logger.info("Copying data from %s..." % name)
+            # Sanity check initialrev and turn it into hash (required for copying history,
+            # because resolving a name ref only works in the component repo).
+            rev = runcmd('git rev-parse %s' % initialrev, ldir).strip()
+            if rev != initialrev:
+                try:
+                    refs = runcmd('git show-ref -s %s' % initialrev, ldir).split('\n')
+                    if len(set(refs)) > 1:
+                        # Happens for example when configured to track
+                        # "master" and there is a refs/heads/master. The
+                        # traditional behavior from "git archive" (preserved
+                        # here) it to choose the first one. This might not be
+                        # intended, so at least warn about it.
+                        logger.warn("%s: initial revision '%s' not unique, picking result of rev-parse = %s" %
+                                    (name, initialrev, refs[0]))
+                        initialrev = rev
+                except:
+                    # show-ref fails for hashes. Skip the sanity warning in that case.
+                    pass
+                initialrev = rev
             dest_dir = repo['dest_dir']
             if dest_dir and dest_dir != ".":
                 extract_dir = os.path.join(os.getcwd(), dest_dir)

@@ -213,22 +238,155 @@ def action_init(conf, args):
             else:
                 extract_dir = os.getcwd()
             file_filter = repo.get('file_filter', "")
-            files = runcmd("git archive %s | tar -x -v -C %s %s" % (initialrev, extract_dir, file_filter), ldir)
             exclude_patterns = repo.get('file_exclude', '').split()
-            if exclude_patterns:
-                # Implement file removal by letting tar create the
-                # file and then deleting it in the file system
-                # again. Uses the list of files created by tar (easier
-                # than walking the tree).
-                for file in files.split('\n'):
-                    for pattern in exclude_patterns:
-                        if fnmatch.fnmatch(file, pattern):
-                            os.unlink(os.path.join(extract_dir, file))
-                            break
+            def copy_selected_files(initialrev, extract_dir, file_filter, exclude_patterns, ldir,
+                                    subdir=""):
+                # When working inside a filtered branch which had the
+                # files already moved, we need to prepend the
+                # subdirectory to all filters, otherwise they would
+                # not match.
+                if subdir:
+                    file_filter = ' '.join([subdir + '/' + x for x in file_filter.split()])
+                    exclude_patterns = [subdir + '/' + x for x in exclude_patterns]
+                # To handle both cases, we cd into the target
+                # directory and optionally tell tar to strip the path
+                # prefix when the files were already moved.
+                subdir_components = len(os.path.normpath(subdir).split(os.path.sep)) if subdir else 0
+                strip=('--strip-components=%d' % subdir_components) if subdir else ''
+                # TODO: file_filter wild cards do not work (and haven't worked before either), because
+                # a) GNU tar requires a --wildcards parameter before turning on wild card matching.
+                # b) The semantic is not as intendend (src/*.c also matches src/foo/bar.c,
+                #    in contrast to the other use of file_filter as parameter of "git archive"
+                #    where it only matches .c files directly in src).
+                files = runcmd("git archive %s %s | tar -x -v %s -C %s %s" %
+                               (initialrev, subdir,
+                                strip, extract_dir, file_filter),
+                               ldir)
+                if exclude_patterns:
+                    # Implement file removal by letting tar create the
+                    # file and then deleting it in the file system
+                    # again. Uses the list of files created by tar (easier
+                    # than walking the tree).
+                    for file in files.split('\n'):
+                        for pattern in exclude_patterns:
+                            if fnmatch.fnmatch(file, pattern):
+                                os.unlink(os.path.join(*([extract_dir] + ['..'] * subdir_components + [file])))
+                                break
+
+            if not conf.history:
+                copy_selected_files(initialrev, extract_dir, file_filter, exclude_patterns, ldir)
+            else:
+                # First fetch remote history into local repository.
+                # We need a ref for that, so ensure that there is one.
+                refname = "combo-layer-init-%s" % name
+                runcmd("git branch -f %s %s" % (refname, initialrev), ldir)
+                runcmd("git fetch %s %s" % (ldir, refname))
+                runcmd("git branch -D %s" % refname, ldir)
+                # Make that the head revision.
+                runcmd("git checkout -b %s %s" % (name, initialrev))
+                # Optional: rewrite history to change commit messages or to move files.
+                if 'hook' in repo or dest_dir and dest_dir != ".":
+                    filter_branch = ['git', 'filter-branch', '--force']
+                    with tempfile.NamedTemporaryFile() as hookwrapper:
+                        if 'hook' in repo:
+                            # Create a shell script wrapper around the original hook that
+                            # can be used by git filter-branch. Hook may or may not have
+                            # an absolute path.
+                            hook = repo['hook']
+                            hook = os.path.join(os.path.dirname(conf.conffile), '..', hook)
+                            # The wrappers turns the commit message
+                            # from stdin into a fake patch header.
+                            # This is good enough for changing Subject
+                            # and commit msg body with normal
+                            # combo-layer hooks.
+                            hookwrapper.write('''set -e
+tmpname=$(mktemp)
+trap "rm $tmpname" EXIT
+echo -n 'Subject: [PATCH] ' >>$tmpname
+cat >>$tmpname
+if ! [ $(tail -c 1 $tmpname | od -A n -t x1) == '0a' ]; then
+    echo >>$tmpname
+fi
+echo '---' >>$tmpname
+%s $tmpname $GIT_COMMIT %s
+tail -c +18 $tmpname | head -c -4
+''' % (hook, name))
+                            hookwrapper.flush()
+                            filter_branch.extend(['--msg-filter', 'bash %s' % hookwrapper.name])
+                        if dest_dir and dest_dir != ".":
+                            parent = os.path.dirname(dest_dir)
+                            if not parent:
+                                parent = '.'
+                            # May run outside of the current directory, so do not assume that .git exists.
+                            filter_branch.extend(['--tree-filter', 'mkdir -p .git/tmptree && mv $(ls -1 -a | grep -v -e ^.git$ -e ^.$ -e ^..$) .git/tmptree && mkdir -p %s && mv .git/tmptree %s' % (parent, dest_dir)])
+                        filter_branch.append('HEAD')
+                        runcmd(filter_branch)
+                        runcmd('git update-ref -d refs/original/refs/heads/%s' % name)
+                repo['rewritten_revision'] = runcmd('git rev-parse HEAD').strip()
+                repo['stripped_revision'] = repo['rewritten_revision']
+                # Optional filter files: remove everything and re-populate using the normal filtering code.
+                # Override any potential .gitignore.
+                if file_filter or exclude_patterns:
+                    runcmd('git rm -rf .')
+                    if not os.path.exists(extract_dir):
+                        os.makedirs(extract_dir)
+                    copy_selected_files('HEAD', extract_dir, file_filter, exclude_patterns, '.',
+                                        subdir=dest_dir if dest_dir and dest_dir != '.' else '')
+                    runcmd('git add --all --force .')
+                    if runcmd('git status --porcelain'):
+                        # Something to commit.
+                        runcmd(['git', 'commit', '-m',
+                                '''%s: select file subset
+
+Files from the component repository were chosen based on
+the following filters:
+file_filter = %s
+file_exclude = %s''' % (name, file_filter or '<empty>', repo.get('file_exclude', '<empty>'))])
+                        repo['stripped_revision'] = runcmd('git rev-parse HEAD').strip()
+
             if not lastrev:
-                lastrev = runcmd("git rev-parse %s" % initialrev, ldir).strip()
+                lastrev = runcmd('git rev-parse %s' % initialrev, ldir).strip()
                 conf.update(name, "last_revision", lastrev, initmode=True)
-        runcmd("git add .")
+
+        if not conf.history:
+            runcmd("git add .")
+        else:
+            # Create Octopus merge commit according to http://stackoverflow.com/questions/10874149/git-octopus-merge-with-unrelated-repositoies
+            runcmd('git checkout master')
+            merge = ['git', 'merge', '--no-commit']
+            with open('.git/info/grafts', 'w') as grafts:
+                grafts.write('%s\n' % startrev)
+                for name in conf.repos:
+                    repo = conf.repos[name]
+                    # Use branch created earlier.
+                    merge.append(name)
+                    for start in runcmd('git log --pretty=format:%%H --max-parents=0 %s' % name).split('\n'):
+                        grafts.write('%s %s\n' % (start, startrev))
+            try:
+                runcmd(merge)
+            except Exception, error:
+                logger.info('''Merging component repository history failed, perhaps because of merge conflicts.
+It may be possible to commit anyway after resolving these conflicts.
+
+%s''' % error)
+            # Create MERGE_HEAD and MERGE_MSG. "git merge" itself
+            # does not create MERGE_HEAD in case of a (harmless) failure,
+            # and we want certain auto-generated information in the
+            # commit message for future reference and/or automation.
+            with open('.git/MERGE_HEAD', 'w') as head:
+                with open('.git/MERGE_MSG', 'w') as msg:
+                    msg.write('repo: initial import of components\n\n')
+                    # head.write('%s\n' % startrev)
+                    for name in conf.repos:
+                        repo = conf.repos[name]
+                        # <upstream ref> <rewritten ref> <rewritten + files removed>
+                        msg.write('combo-layer-%s: %s %s %s\n' % (name,
+                                                                  repo['last_revision'],
+                                                                  repo['rewritten_revision'],
+                                                                  repo['stripped_revision']))
+                        rev = runcmd('git rev-parse %s' % name).strip()
+                        head.write('%s\n' % rev)
+
         if conf.localconffile:
             localadded = True
             try:

@@ -631,6 +789,9 @@ Action:
     parser.add_option("-n", "--no-pull", help = "skip pulling component repos during update",
                action = "store_true", dest = "nopull", default = False)
 
+    parser.add_option("-H", "--history", help = "import full history of components during init",
+                      action = "store_true", default = False)
+
     options, args = parser.parse_args(sys.argv)
 
     # Dispatch to action handler

index d11274e..6d24ce3 100755
@@ -354,14 +354,14 @@ file_exclude = %s''' % (name, file_filter or '<empty>', repo.get('file_exclude',
             # Create Octopus merge commit according to http://stackoverflow.com/questions/10874149/git-octopus-merge-with-unrelated-repositoies
             runcmd('git checkout master')
             merge = ['git', 'merge', '--no-commit']
-            with open('.git/info/grafts', 'w') as grafts:
-                grafts.write('%s\n' % startrev)
-                for name in conf.repos:
-                    repo = conf.repos[name]
-                    # Use branch created earlier.
-                    merge.append(name)
-                    for start in runcmd('git log --pretty=format:%%H --max-parents=0 %s' % name).split('\n'):
-                        grafts.write('%s %s\n' % (start, startrev))
+            for name in conf.repos:
+                repo = conf.repos[name]
+                # Use branch created earlier.
+                merge.append(name)
+                # Root all commits which have no parent in the common
+                # ancestor in the new repository.
+                for start in runcmd('git log --pretty=format:%%H --max-parents=0 %s' % name).split('\n'):
+                    runcmd('git replace --graft %s %s' % (start, startrev))
             try:
                 runcmd(merge)
             except Exception, error:

index 6d24ce3..cbff618 100755
@@ -284,6 +284,46 @@ def action_init(conf, args):
                 runcmd("git branch -D %s" % refname, ldir)
                 # Make that the head revision.
                 runcmd("git checkout -b %s %s" % (name, initialrev))
+                # Optional: cut the history by replacing the given
+                # start point(s) with commits providing the same
+                # content (aka tree), but with commit information that
+                # makes it clear that this is an artifically created
+                # commit and nothing the original authors had anything
+                # to do with.
+                since_rev = repo.get('since_revision', '')
+                if since_rev:
+                    committer = runcmd('git var GIT_AUTHOR_IDENT').strip()
+                    # Same time stamp, no name.
+                    author = re.sub('.* (\d+ [+-]\d+)', r'unknown <unknown> \1', committer)
+                    logger.info('author %s' % author)
+                    for rev in since_rev.split():
+                        # Resolve in component repo...
+                        rev = runcmd('git log --oneline --no-abbrev-commit -n1 %s' % rev, ldir).split()[0]
+                        # ... and then get the tree in current
+                        # one. The commit should be in both repos with
+                        # the same tree, but better check here.
+                        tree = runcmd('git show -s --pretty=format:%%T %s' % rev).strip()
+                        with tempfile.NamedTemporaryFile() as editor:
+                            editor.write('''cat >$1 <<EOF
+tree %s
+author %s
+committer %s
+
+%s: squashed import of component
+
+This commit copies the entire set of files as found in
+%s %s
+
+For more information about previous commits, see the
+upstream repository.
+
+Commit created by combo-layer.
+EOF
+''' % (tree, author, committer, name, name, since_rev))
+                            editor.flush()
+                            os.environ['GIT_EDITOR'] = 'sh %s' % editor.name
+                            runcmd('git replace --edit %s' % rev)
+
                 # Optional: rewrite history to change commit messages or to move files.
                 if 'hook' in repo or dest_dir and dest_dir != ".":
                     filter_branch = ['git', 'filter-branch', '--force']

index 38bc53c..90e2b58 100644
@@ -63,11 +63,24 @@ last_revision =
 # example:
 #     hook = combo-layer-hook-default.sh
 
+# since_revision:
+#   since_revision = release-1-2
+#   since_revision = 12345 abcdf
+#
+# If provided, truncate imported history during "combo-layer --history
+# init" at the specified revision(s).  More than one can be specified
+# to cut off multiple component branches.
+#
+# The specified commits themselves do not get imported. Instead, an
+# artificial commit with "unknown" author is created with a content
+# that matches the original commit.
+
 [oe-core]
 src_uri = git://git.openembedded.org/openembedded-core
 local_repo_dir = /home/kyu3/src/test/oecore
 dest_dir = .
 last_revision =
+since_revision = some-tag-or-commit-on-master-branch
 
 # It is also possible to embed python code in the config values. Similar
 # to bitbake it considers every value starting with @ to be a python

index 8b148ac..9dd5aed 100755
@@ -9,5 +9,5 @@ patchfile=$1
 rev=$2
 reponame=$3
 
-sed -i -e "s#^Subject: \[PATCH\] \(.*\)#Subject: \[PATCH\] $reponame: \1#" $patchfile
+sed -i -e "s#^Subject: \[PATCH\] \($reponame: \)*\(.*\)#Subject: \[PATCH\] $reponame: \2#" $patchfile
 sed -i -e "0,/^Signed-off-by:/s#\(^Signed-off-by:.*\)#\($reponame rev: $rev\)\n\n\1#" $patchfile

index 9dd5aed..46f2b70 100755
@@ -9,5 +9,5 @@ patchfile=$1
 rev=$2
 reponame=$3
 
-sed -i -e "s#^Subject: \[PATCH\] \($reponame: \)*\(.*\)#Subject: \[PATCH\] $reponame: \2#" $patchfile
+sed -i -e "0,/^Subject:/s#^Subject: \[PATCH\] \($reponame: \)*\(.*\)#Subject: \[PATCH\] $reponame: \2#" $patchfile
 sed -i -e "0,/^Signed-off-by:/s#\(^Signed-off-by:.*\)#\($reponame rev: $rev\)\n\n\1#" $patchfile

index 46f2b70..1e3a3b9 100755
@@ -10,4 +10,11 @@ rev=$2
 reponame=$3
 
 sed -i -e "0,/^Subject:/s#^Subject: \[PATCH\] \($reponame: \)*\(.*\)#Subject: \[PATCH\] $reponame: \2#" $patchfile
-sed -i -e "0,/^Signed-off-by:/s#\(^Signed-off-by:.*\)#\($reponame rev: $rev\)\n\n\1#" $patchfile
+if grep -q '^Signed-off-by:' $patchfile; then
+    # Insert before Signed-off-by.
+    sed -i -e "0,/^Signed-off-by:/s#\(^Signed-off-by:.*\)#\(From $reponame rev: $rev\)\n\n\1#" $patchfile
+else
+    # Insert before final --- separator, with extra blank lines removed.
+    perl -e "\$_ = join('', <>); s/^(.*\S[ \t]*)(\n|\n\s*\n)---\n/\$1\n\nFrom $reponame rev: $rev\n---\n/s; print;" $patchfile >$patchfile.tmp
+    mv $patchfile.tmp $patchfile
+fi