different prefixes (although this is only lightly tested).
---

Many things have changed, time for a repost. It no long needs the
"restore --match" patches. 

 contrib/nmbug |  565 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 565 insertions(+), 0 deletions(-)
 create mode 100755 contrib/nmbug

diff --git a/contrib/nmbug b/contrib/nmbug
new file mode 100755
index 0000000..2128b95
--- /dev/null
+++ b/contrib/nmbug
@@ -0,0 +1,565 @@
+#!/usr/bin/env perl
+# Copyright (c) 2011 David Bremner
+# License: same as notmuch
+
+use strict;
+use File::Path qw(remove_tree make_path);
+use File::Temp qw(tempdir tempfile);
+use File::Basename;
+use Pod::Usage;
+
+no encoding;
+
+my $NMBGIT = $ENV{NMBGIT} || $ENV{HOME}."/.nmbug";
+
+$NMBGIT .= '/.git' if (-d $NMBGIT.'/.git');
+
+my $TAGPREFIX = $ENV{NMBPREFIX} || "notmuch::";
+
+# magic hashes for git
+my $EMPTYBLOB = 'e69de29bb2d1d6434b8b29ae775ad8c2e48c5391';
+my $EMPTYTREE = '4b825dc642cb6eb9a060e54bf8d69288fbee4904';
+
+# for encoding
+
+my $ESCAPE_CHAR='%';
+my $NO_ESCAPE= "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+-_@=.:,";
+my $MUST_ENCODE=qr{[^\Q$NO_ESCAPE\E]};
+my $ESCAPED_RX=qr{$ESCAPE_CHAR[A-Fa-f0-9]{2}};
+
+my %command=(
+	     archive	=> \&do_archive,
+	     checkout	=>\&do_checkout,
+	     commit	=> \&do_commit,
+	     fetch	=> \&do_fetch,
+	     help	=> \&do_help,
+	     log	=> \&do_log,
+	     merge	=> \&do_merge,
+	     pull	=> \&do_pull,
+	     push	=> \&do_push,
+	     status	=> \&do_status,
+	     );
+
+my $subcommand=shift;
+
+if (!exists $command{$subcommand}){
+  usage();
+}
+
+&{$command{$subcommand}}(@ARGV);
+
+sub get_tags {
+  my $prefix=shift;
+  my @tags;
+  open my $fh, 'notmuch search --output=tags "*"|' or die "error dumping tags";
+  while (<$fh>) {
+    chomp();
+    push @tags, $_ if (m/^$prefix/);
+  }
+  return @tags;
+}
+
+sub do_archive {
+  system ('git', "--git-dir=$NMBGIT", 'archive', 'HEAD');
+}
+
+sub is_committed(){
+  my $status = compute_status();
+  return scalar (@{$status->{added}} ) + scalar (@{$status->{deleted}} )==0
+}
+
+sub do_commit {
+  my @args=@_;
+
+  if ( is_committed() ){
+    print "Nothing to commit\n";
+    return;
+  }
+
+  my $index=index_tags();
+
+  my $tree= git ('write-tree', { GIT_INDEX_FILE=>$index })
+    or die "no output from write-tree";
+
+  my $parent = git ( 'rev-parse', 'HEAD'  )
+    or die "no output from rev-parse";
+
+  my $commit = git ('commit-tree', $tree, '-p', $parent, {},  @args);
+
+  git ('update-ref', 'HEAD', $commit);
+
+  unlink $index || die "unlink: $!";
+
+}
+
+sub do_fetch {
+  my $remote = shift || "origin";
+
+  git ('fetch', $remote);
+}
+
+sub git {
+
+  return subcommand('git',@_);
+
+}
+
+sub subcommand {
+  die 'command and subcommand needed' unless (scalar(@_) >= 2);
+
+  return run (@_);
+}
+
+# arguments are any number of strings for ARGV, an optional hash ref
+# for settings for the environment, followed by any number of strings as 
+# as lines for stdin.
+
+sub run {
+
+  my $command=shift 
+    or die "command not specified";
+
+  my @args;
+
+
+  while ( scalar(@_) && !ref($_[0]) ) {
+    push @args, shift;
+  };
+
+  my %SETENV={};
+  if(ref($_[0]) eq 'HASH'){
+    my $ref=shift;
+    %SETENV=%{$ref};
+  }
+
+  $SETENV{GIT_DIR} ||= $NMBGIT;
+
+  my @input=@_;
+  my @output;
+
+  my $pid = open my $child, '-|';
+  if ($pid){
+    while(<$child>){
+      chomp();
+      push @output,$_;
+    }
+    close ($child);
+  } else {
+
+    # setup child environment
+    while (my ($key,$val) = each %SETENV) {
+      $ENV{$key}=$val;
+    }
+
+    read_from(@input);
+    exec($command,@args) || die "exec $command @args: $!";
+  }
+
+  if (wantarray()) {
+    return @output;
+  }
+  elsif (defined wantarray()) {
+    return join("\n",@output);
+  }
+  else {
+    return;
+  }
+}
+
+sub read_from {
+    close STDIN;
+    if (!scalar(@_)){
+      open STDIN, '<', '/dev/null' || die "reopening stdin: $!";
+    } else {
+      my ($fh,$tempfile) = tempfile();
+      foreach my $line (@_){
+	print $fh $line;
+      }
+      close $fh || die "closing";
+
+      open STDIN, '<', $tempfile or
+	die "reopening stdin: $!";
+    }
+}
+
+sub notmuch {
+  my @args=@_;
+  system ('notmuch', @args) == 0 or die  "notmuch @args failed: $?"
+}
+
+
+sub index_tags {
+
+  my $index=$NMBGIT."/nmbug.index";
+
+  my $query = join " ", map ("tag:$_", get_tags($TAGPREFIX));
+  open my $fh, "notmuch dump -- $query|" or die "notmuch dump: $!";
+
+  git ('read-tree', $EMPTYTREE);
+  open my $git, "|GIT_DIR=$NMBGIT GIT_INDEX_FILE=$index git update-index --index-info" or die "git update-index";
+
+  while (<$fh>) {
+    m/ ( [^ ]* ) \s+ \( ([^\)]* ) \) /x || die "syntax error in dump";
+    my ($id,$rest) = ($1,$2);
+    index_tags_for_msg ($git,$id, split(" ", $rest));
+  }
+
+  close $git;
+  return $index;
+}
+
+sub index_tags_for_msg {
+  my $fh=shift;
+  my $msgid = shift;
+  my @tags=@_;
+
+  foreach my $tag (@tags){
+    # insist prefix is there, but remove it before writing
+    next unless ($tag =~ s/^$TAGPREFIX//);
+    my $tagpath = 'tags/' . encode_for_fs($msgid)  . '/' . encode_for_fs ($tag);
+    print $fh "100644 blob $EMPTYBLOB\t$tagpath\n";
+  }
+}
+
+sub do_checkout {
+  do_sync (action => 'checkout');
+}
+
+sub do_sync {
+
+  my %args=@_;
+
+  my $status=compute_status();
+  my ($A_action, $D_action);
+
+  if ($args{action} eq 'checkout') {
+    $A_action = '-';
+    $D_action = '+';
+  } else {
+    $A_action = '+';
+    $D_action = '-';
+  }
+
+  foreach my $pair (@{$status->{added}}){
+
+    notmuch ('tag', $A_action.$TAGPREFIX.$pair->{tag},
+	     'id:'.$pair->{id});
+  }
+
+  foreach my $pair (@{$status->{deleted}}){
+    notmuch ('tag', $D_action.$TAGPREFIX.$pair->{tag},
+	     'id:'.$pair->{id});
+  }
+
+}
+
+sub insist_committed {
+
+  if ( !is_committed () ){
+    print "Uncommitted changes to $TAGPREFIX* tags in notmuch
+
+For a summary of changes, run 'nmbug status'
+To save your changes,     run 'nmbug commit' before merging/pull
+To discard your changes,  run 'nmbug checkout'
+";
+    exit(1);
+  }
+
+}
+
+sub do_pull {
+  my $remote = shift || "origin";
+
+  git ( 'fetch', $remote);
+
+  do_merge();
+}
+
+sub do_merge {
+  insist_committed();
+
+  my $tempwork= tempdir ("/tmp/nmbug-merge.XXXXXX", CLEANUP=>1);
+
+  git ( 'checkout', '-f', 'HEAD', { GIT_WORK_TREE=> $tempwork });
+
+  git ( 'merge', 'FETCH_HEAD', { GIT_WORK_TREE=> $tempwork });
+
+  do_checkout();
+}
+
+sub do_log {
+  # we don't want output trapping here, because we want the pager.
+  system ( 'git', "--git-dir=$NMBGIT", 'log', '--name-status', @_);
+}
+
+sub do_push {
+  my $remote = shift || "origin";
+
+  git ('push', $remote);
+}
+
+sub do_status {
+  my $status = compute_status();
+  
+  foreach my $pair (@{$status->{added}}){
+    printf "A\t%s\t%s\n",$pair->{id}, $pair->{tag};
+  }
+
+  foreach my $pair (@{$status->{deleted}}){
+    printf "D\t%s\t%s\n",$pair->{id}, $pair->{tag};
+  }
+
+  foreach my $id (@{$status->{missing}}){
+    print "U\t$id\n",
+  }
+
+  if (is_unmerged ()) {
+    foreach my $pair (diff_refs('A')){
+      printf "a\t%s\t%s\n",$pair->{id}, $pair->{tag};
+    }
+
+    foreach my $pair (diff_refs('D')){
+      printf "d\t%s\t%s\n",$pair->{id}, $pair->{tag};
+    }
+  }
+
+}
+
+sub is_unmerged {
+  my $fetch_head = git ('rev-parse', 'FETCH_HEAD');
+  my $base = git ( 'merge-base', 'HEAD', 'FETCH_HEAD');
+
+  return ($base ne $fetch_head);
+
+}
+sub compute_status {
+  my %args=@_;
+
+  my @added;
+  my @deleted;
+  my @missing;
+
+  my $index=index_tags();
+
+  my @maybe_deleted = diff_index($index,'D');
+
+  foreach my $pair (@maybe_deleted){
+
+    my $id = $pair->{id};
+
+    open my $fh, "notmuch search --output=files id:$id |"
+      or die "searching for $id";
+    if (!<$fh>) {
+      push @missing, $id;
+    } else {
+      push @deleted, $pair;
+    }
+  }
+
+
+  @added = diff_index ($index, 'A');
+
+  unlink $index || die "unlink $index: $!";
+
+  return { added => [@added], deleted => [@deleted], missing=> [@missing] };
+}
+
+sub diff_index {
+  my $index=shift;
+  my $filter=shift;
+
+  my @lines=git( qw/diff-index --cached/,
+		 "--diff-filter=$filter", qw/--name-only HEAD/,
+		 {GIT_INDEX_FILE=>$index} );
+
+  return unpack_diff_lines(@lines);
+}
+
+sub diff_refs {
+  my $filter=shift;
+  my $ref1 = shift || 'HEAD';
+  my $ref2 = shift || 'FETCH_HEAD';
+
+  my @lines=git( 'diff', "--diff-filter=$filter", '--name-only',
+		 $ref1, $ref2);
+
+  return unpack_diff_lines(@lines);
+}
+
+
+sub unpack_diff_lines {
+  my @found;
+
+  foreach (@_){
+    chomp();
+    my ($id,$tag) = m@tags/ ([^/]+) / ([^/]+) @x;
+
+    $id = decode_from_fs($id);
+    $tag = decode_from_fs($tag);
+
+    push @found, { id => $id, tag => $tag };
+  }
+
+  return @found;
+}
+
+sub encode_for_fs{
+  my $str=shift;
+
+  $str=~ s/($MUST_ENCODE)/"$ESCAPE_CHAR".sprintf("%02x",ord($1))/ge;
+  return $str;
+}
+
+sub decode_from_fs{
+  my $str=shift;
+
+  $str=~ s/$ESCAPED_RX/ hex($1)/eg;
+
+  return $str;
+
+}
+
+
+sub usage {
+  pod2usage();
+  exit(1);
+}
+
+sub do_help {
+  pod2usage( -verbose=>2 );
+  exit(0);
+}
+
+__END__
+
+=head1 NAME
+
+nmbug - manage notmuch tags about notmuch
+
+=head1 SYNOPSIS
+
+nmbug subcommand [options]
+
+B<nmbug help> for more help
+
+=head1 OPTIONS
+
+=head2 Most common commands
+
+=over 8
+
+=item B<commit> [message]
+
+Commit appropriately prefixed tags from the notmuch database to
+git. Any extra arguments are used (one per line) as a commit message.
+
+=item  B<push> [remote]
+
+push local nmbug git state to remote repo
+
+=item  B<pull> [remote]
+
+pull (merge) remote repo changes to notmuch. B<pull> is equivalent to
+B<fetch> followed by B<merge>.
+
+=back
+
+=head2 Other Useful Commands
+
+=over 8
+
+=item B<checkout>
+
+Update the notmuch database from git. This is mainly useful to discard
+your changes in notmuch relative to git.
+
+=item B<fetch> [remote]
+
+Fetch changes from the remote repo (see merge to bring those changes
+into notmuch). 
+
+=item B<help> [subcommand]
+
+print help [for subcommand]
+
+=item B<log> [parameters]
+
+A simple wrapper for git log. After running C<nmbug fetch>, you can
+inspect the changes with C<nmbug log HEAD..FETCH_HEAD>
+
+=item B<merge> 
+
+Merge changes from FETCH_HEAD into HEAD, and load the result into
+notmuch.
+
+=item  B<status>
+
+Show pending updates in notmuch or git repo. See below for more
+information about the output format.
+
+=back
+
+=head2 Less common commands
+
+=over 8
+
+=item B<archive>
+
+Dump a tar archive (using git archive) of the current nmbug tag set.
+
+=back
+
+
+=head1 STATUS FORMAT
+
+B<nmbug status> prints lines of the form
+
+   c Message-Id tag
+
+where c is
+
+=over 8
+
+=item B<A>
+
+Tag is present in notmuch database, but not committed to nmbug
+(equivalently, tag has been deleted in nmbug repo, e.g. by a pull, but
+not restored to notmuch database).
+
+=item B<a>
+
+Tag is fetched, but not merged into notmuch.
+
+=item B<D>
+
+Tag is present in nmbug repo, but not restored to notmuch database
+(equivalently, tag has been deleted in notmuch)
+
+=item B<d>
+
+Tag deletion is fetched, but not merged into notmuch.
+
+=item B<U>
+
+Message is unknown (missing from local notmuch database)
+
+=back
+
+=head1 DUMP FORMAT
+
+Each tag $tag for message with Message-Id $id is written to
+an empty file
+
+	tags/encode($id)/encode($tag)
+
+The encoding preserves alphanumerics, and the characters "+-_@=.:,"
+(not the quotes).  All other octets are replaced with '%' followed by
+a two digit hex number.
+
+=head1 ENVIRONMENT
+
+B<NMBGIT> specifies the location of the git repository used by nmbug. 
+If not specified $HOME/.nmbug is used.
+
+B<NMBPREFIX> specifies the prefix in the notmuch database for tags of
+interest to nmbug. If not specified 'notmuch::' is used.

