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/usr/bin/mtn-cleanup is in monotone-extras 1.0-12.

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The actual contents of the file can be viewed below.

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#!/usr/bin/env perl
##############################################################################
#
#   File Name    - mtn-cleanup
#
#   Description  - Remove all extra files from a Monotone workspace and then
#                  revert the revision based files.
#
#   Author       - A.E.Cooper.
#
#   Legal Stuff  - Copyright (c) 2007 Anthony Edward Cooper
#                  <aecooper@coosoft.plus.com>.
#
#                  This program is free software; you can redistribute it
#                  and/or modify it under the terms of the GNU General Public
#                  License as published by the Free Software Foundation;
#                  either version 3 of the License, or (at your option) any
#                  later version.
#
#                  This program is distributed in the hope that it will be
#                  useful, but WITHOUT ANY WARRANTY; without even the implied
#                  warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
#                  PURPOSE. See the GNU General Public License for more
#                  details.
#
#                  You should have received a copy of the GNU General Public
#                  License along with this software; if not, write to the Free
#                  Software Foundation, Inc., 59 Temple Place - Suite 330,
#                  Boston, MA 02111-1307 USA.
#
##############################################################################
#
##############################################################################
#
#   GLOBAL DATA FOR THIS MODULE
#
##############################################################################



# ***** DIRECTIVES *****

require 5.008005;

use strict;
use English;
use integer;
use warnings;

# ***** REQUIRED PACKAGES *****

use File::Basename;
use File::Spec;

# ***** GLOBAL DATA DECLARATIONS *****

# The name of this script.

use constant SCRIPT => basename($PROGRAM_NAME);

# The manifest hit list hash. The key is the file name relative to the
# work-space, the value is unimportant. If you do a lookup of a file against
# this hash and the result is defined then that file exists in the Monotone
# manifest.

my %manifest;

# ***** FUNCTIONAL PROTOTYPES FOR THIS FILE *****

sub cleanup_workspace($);
sub get_manifest_hit_list($);
#
##############################################################################
#
#   Routine      - Main Body Of Code
#
#   Description  - This is the main body of code for the tools script.
#
#   Data         - @_           : The command line arguments.
#                  Return Value : Unix exit code.
#
##############################################################################



my $response;

# First check that we are at the top level of a Monotone work-space.

if (! -d "_MTN")
{
    printf(STDERR
	   "%s: This command must be run from the work-space's base "
	       . "directory.\n",
	   SCRIPT);
    exit(1);
}

# This is a dangerous command to run, so warn the user.

printf("%s: Warning - This will remove all files that have not been "
           . "committed.\n",
       SCRIPT);
printf("Proceed (Y/N)[N]: ");
$response = readline(STDIN);
chomp($response);
if ($response =~ m/^[yY]$/)
{
    get_manifest_hit_list(\%manifest);
    cleanup_workspace("");
    printf("Now reverting files...\n");
    system("mtn", "revert", ".");
}

exit 0;
#
##############################################################################
#
#   Routine      - cleanup_workspace
#
#   Description  - Traverse the workspace removing anything that isn't listed
#                  in the manifest.
#
#   Data         - $directory : The directory that is to be cleaned.
#
##############################################################################



sub cleanup_workspace($)
{

    my ($directory) = @_;

    my ($dir_handle,
	$file,
	@files,
	$rel_path);

    if ($directory eq "")
    {
	opendir($dir_handle, ".") or die("opendir failed: $!");
    }
    else
    {
	opendir($dir_handle, $directory) or die("opendir failed: $!");
    }
    @files = sort readdir($dir_handle);
    close($dir_handle);

    foreach $file (@files)
    {
	if ($directory eq "")
	{
	    $rel_path = $file;
	}
	else
	{
	    $rel_path = File::Spec->catfile($directory, $file);
	}
	if (-d $rel_path)
	{
	    if ($file ne "." && $file ne ".." && $file ne "_MTN")
	    {
		if ($manifest{$rel_path})
		{
		    cleanup_workspace($rel_path);
		}
		else
		{
		    printf("Removing directory %s...\n", $rel_path);
		    system("/bin/rm", "-rf", $rel_path);
		}
	    }
	}
	else
	{
	    if (! $manifest{$rel_path})
	    {
		printf("Removing file %s...\n", $rel_path);
		unlink($rel_path);
	    }
	}
    }

}
#
##############################################################################
#
#   Routine      - get_manifest_hit_list
#
#   Description  - Generates a boolean hash keyed on manifest file names, the
#                  value is not important but is just set to 1.
#
#   Data         - $manifest_ref : A reference to a hash that is to contain
#                                  the manifest hit list hash.
#
##############################################################################



sub get_manifest_hit_list($)
{

    my ($manifest_ref) = @_;

    my ($entry,
	$handle,
        $line,
        $rev_id);

    %$manifest_ref = ();

    $rev_id = `mtn automate get_base_revision_id 2> /dev/null`
	or die("mtn automate get_base_revision_id failed: $!");
    chomp($rev_id);

    open($handle, "-|", "mtn automate get_manifest_of " . $rev_id)
	or die("open failed: $!");
    for ($line = readline($handle); $line; $line = readline($handle))
    {
	chomp($line);
	$entry = undef;
	if ($line =~ m/^   file \"/)
	{
	    ($entry) = ($line =~ m/^   file \"([^\"]+)\"$/);
	}
	if ($line =~ m/^dir \"/)
	{
	    ($entry) = ($line =~ m/^dir \"([^\"]+)\"$/);
	}
	if ($entry)
	{
	    $$manifest_ref{$entry} = 1;
	}
    }
    close($handle);

}