wiggle.1

.\" -*- nroff -*-
.\" wiggle - apply rejected patches
.\"
.\" Copyright (C) 2003 Neil Brown <neilb@cse.unsw.edu.au>
.\" Copyright (C) 2010-2013 Neil Brown <neilb@suse.de>
.\" Copyright (C) 2018-2020 Neil Brown <neil@brown.name>
.\"
.\"
.\"    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 2 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 program.
.\"
.\"    Author: Neil Brown
.\"    Email: <neil@brown.name>
.\"
.TH WIGGLE 1 "" v1.3
.SH NAME
wiggle \- apply rejected patches and perform word-wise diffs
.SH SYNOPSIS
.BI wiggle " [function] [options] file [files]"
.SH DESCRIPTION
The main function of
.I wiggle
is to apply a patch to a file in a similar manner to the
.BR patch (1)
program.
.P
The distinctive difference of
.I wiggle
is that it will attempt to apply a patch even if the "before" part of
the patch doesn't match the target file perfectly.
This is achieved by breaking the file and patch into words and finding
the best alignment of words in the file with words in the patch.
Once this alignment has been found, any differences (word-wise) in the
patch are applied to the file as best as possible.
.P
Also,
.I wiggle
will (in some cases) detect changes that have already been applied,
and will ignore them.
.P
.I wiggle
ensures that every change in the patch is applied to the target
file somehow.  If a particular change cannot be made in the file, the
file is annotated to show where the change should be made in a similar
way to the
.BR merge (1)
program with the
.B \-A
option.
Each annotation contains 3 components: a portion of the original file
where the change should be applied, a portion of the patch that
couldn't be matched precisely in the file, and the text that should
replace that portion of the patch.  These are separated by lines
containing precisely 7 identical characters, either '<', '|', '=',
or '>', possibly followed by a descriptive word. So
.in +5
.nf
.ft CW
<<<<<<< found
Some portion of the original file
||||||| expected
text to replace
=======
text to replace it with
>>>>>>> replacement
.ft
.fi
.in -5
indicates that "text to replace" should be replaced by "text to
replace it with" somewhere in the portion of the original file.
However
.I wiggle
was not able to find a place to make this change.
.P
.I wiggle
can also produce conflict reports showing only the words that are
involved rather than showing whole lines.
In this case the output looks like:
.ft CW
.ti +5
<<<---original|||old===new--->>>
.ft
.P
One possible usage of
.I wiggle
is to run
.I patch
to apply some patch, and to collect a list of rejects by monitoring
the error messages from patch.  Then for each file for which a
reject was found, run
.ti +5
wiggle \-\-replace originalfile originalfile.rej
.P
Finally each file must be examined to resolve any unresolved
conflicts, and to make sure the applied patch is semantically correct.
.P
Alternately, the original patch file can be fed to the
.B browse
mode as
.ti +5
wiggle \-B < patchfile
.P
This will allow the changes and conflicts to be inspected and, to some
extent, modified; and then the results can be saved.
.SS OPTIONS
The following options are understood by
.IR wiggle .
Some of these are explained in more detail in the following sections
on MERGE, DIFF, EXTRACT, and BROWSE.
.TP
.BR \-m ", " \-\-merge
Select the "merge" function.  This is the default function.
.TP
.BR \-d ", " \-\-diff
Select the "diff" function.  This displays the differences between
files.  This can be given after
.B \-\-browse
(see below) in which case a patch or diff of two files can be viewed
without the originals.
.TP
.BR \-x ", " \-\-extract
Select the "extract" function.  This extracts one branch of a patch or
merge file.
.TP
.BR \-B ", " \-\-browse
Select the "browse" function.  This is similar to "merge" (or "diff")
only with a different presentation.  Instead of the result simply
being sent to standard output, it is presented using an ncurses-based
GUI so that each hunk of the patch can be examined to understand what
conflicts where involved and what needed to be ignored in order of the
patch to be wiggled in to place.
.TP
.BR \-w ", " \-\-words
Request that all operations and display be word based.  This is the
default for the "diff" function.
.TP
.BR \-\-non\-space
Request that words be defined as sequences of non-white-space.  Without
this flag words are sequences of alphanumerics or single non-white-space
characters.  This flag is enabled by automatically enabled if 
.I wiggle
needs to compare two files which both have more than 50,000 words.
.TP
.BR \-l ", " \-\-lines
Request that all operations and display be line based.
.TP
.BR \-b ", " \-\-ignore\-blanks
De-emphasise white space (space, tab, and newline) is determining
differences and changes.
.RS
.P
Normally white space is treated like a word which can be matched or
changed by a patch.  When this flag is in force, white space serves
only as a separator between other words and is not matched itself.
The effect of this is that changes in the amount of white space are
not treated as significant.
.P
To be precise, any white space is combined with the preceding word
or, in the case of leading space on a line, with the following word.
However it is not involved in any comparisons of that word.  If a patch
deletes a word, the attached white space is deleted as well.  If a
patch adds a word, the attached white space is added as well.
.P
An empty line, or one that contains only blanks, will be treated as a
single word that will match any other blank line, no matter how many
spaces it has.
.P
.B \-b
has no effect in
.B \-\-line
mode.
.RE
.TP
.BR \-p ", " \-\-patch
Treat the last named file as a patch instead of a file (with \-\-diff)
or a merge (\-\-extract).
In
.I merge
or
.B browse
mode,
.B \-p
requires there be exactly one file which is a patch and which can
contain patches to multiple files.  The patches are merged into each
file.  When used in
.I merge
mode, this usage requires the
.B \-\-replace
option as writing lots of merged files to standard-out is impractical.
.RS
.P
When processing a multi-file patch,
.B \-p
can be followed by a numeric argument indicating how many file name
components should be stripped from files named in the patch file.  If no
numeric argument is given,
.I wiggle
will deduce an appropriate number based what files are present in the
filesystem.
.RE
.TP
.BR \-r ", " \-\-replace
Normally the merged output is written to standard-output.  With
.BR \-\-replace ,
the original file is replaced with the merge output.
In
.B browse
mode, this instructs
.I wiggle
to always save the resulting merge when exiting.
.TP
.B \-\-no-backup
Normally when an original file is replaced with the merged result, that
file is renamed to have a ".porig" extension, so that it is preserved.
If you don't want to keep the original, use this option to suppress
the backup.
.TP
.BR \-o ", " \-\-output=
Rather than writing the result to stdout or to replace the original
file, this requests that the output be written to the given file.
This is only meaningful with
.B \-\-merge
or
.B \-\-browse
when given a single merge to browse.
.RS
.P
This option overrides
.BR \-r .
.RE
.TP
.BR \-R ", " \-\-reverse
When used with the
.B diff
function, swap the files before calculating
the differences.
When used with the
.B merge
or
.B browse
functions,
.I wiggle
attempts to revert changes rather than apply them.
.TP
.BR \-\-shortest
If the files being compared are large, it can take a long time to
isolate the differences.  Normally 
.I wiggle
will give up on perfection if a step take more than 20msec.  To over-ride
this and always find the shortest edit-distance between two files, use the
.B \-\-shortest
option.
.TP
.BR \-i ", " \-\-no\-ignore
Normally wiggle will ignore changes in the patch which appear to
already have been applied in the original.  With this flag those
changes are reported as conflicts rather than being ignored.
.TP
.BR \-W ", " \-\-show\-wiggles
When used with
.BR \-\-merge ,
conflicts that can be wiggled into place are reported as conflicts
with an extra stanza which shows what the result would be if this flag
had not been used.  The extra stanza is introduce with a line
containing 7 ampersand
.RB ( & )
characters thus:
.in +5
.nf
.ft CW
<<<<<<< found
Some portion of the original file
||||||| expected
text to replace
=======
text to replace it with
&&&&&&& resolution
Text that would result from a successful wiggle
>>>>>>> replacement
.ft
.fi
.in -5
.TP
.B \-\-report\-wiggles
If a merge is successful in applying all changes, it will normally exit
with a success status (0), only reporting failure (1) if a conflict
occurred and was annotated.  With
.B \-\-report\-wiggles
.I wiggle
will also report failure if any changes had to be wiggled in.  This
can be useful when
.I wiggle
is used for automatic merges as with
.IR git .
If any wiggles happen,
.I git
will report the failure, and the results can be examined to confirm
they are acceptable.
.TP
.BR \-h ", " \-\-help
Print a simple help message.  If given after one of the function
selectors
.RB ( \-\-merge ,
.BR \-\-diff ,
.BR \-\-extract ,
.BR \-\-browse )
help specific to that function is displayed.
.TP
.BR \-V ", " \-\-version
Display the version number of
.IR wiggle .
.TP
.BR \-v ", " \-\-verbose
Enable verbose mode.  Currently this makes no difference.
.TP
.BR \-q ", " \-\-quiet
Enable quiet mode.  This suppresses the message from the merge
function when there are unresolvable conflicts.
.SS WORDS
.I wiggle
can divide a text into lines or words when performing it's tasks.
A line is simply a string of characters terminated by a newline.
A word is either a maximal contiguous string of alphanumerics
(including underscore), a maximal contiguous string of space or tab
characters, or any other single character.
.SS MERGE
The merge function modifies a given text by finding all changes between
two other texts and imposing those changes on the given text.
.P
Normally
.I wiggle
focuses on which words have changed so as to maximise the possibility
of finding a good match in the given text for the context of a given
change.  However it can consider only whole lines instead.
.P
.I wiggle
extracts the three texts that it needs from files listed on the
command line.  Either 1, 2, or 3 files may be listed, and any one of
them may be a lone hyphen signifying standard-input.
.P
If one file is given and the
.B \-p
option is not present, the file is treated as a
.B merge
file, i.e. the output of "merge \-A" or "wiggle".  Such a file
implicitly contains three streams and these are extracted and
compared.
.P
If two files are given, then the first simply contains the primary
text, and the second is treated as a patch file (the output of "diff\ \-u"
or "diff\ \-c", or a ".rej" file from
.IR patch )
and the two other texts
are extracted from that.
.P
If one file is given together with the
.B \-p
option, the file is treated as a patch file containing the names of
the files that it patches.  In this case multiple merge operations can
happen and each takes one stream from a file named in the patch, and
the other two from the patch itself.  The
.B \-\-replace
option is required and the results are written back to the
target files.
.P
Finally if three files are listed, they are taken to contain the given
text and the two other texts, in order.
.P
Normally the result of the merge is written to standard-output.
If the
.B \-r
flag is given, the output is written to a file
which replaces the original given file. In this case the original file
will normally be renamed to have a
.B .porig
suffix (for "patched original" which makes sense if you first use
.I patch
to apply a patch, and then use
.I wiggle
to wiggle the rejects in).  This can be suppressed with the
.B \-\-no\-backup
uption.
.P
Further if the
.B -o
option is given with a file name, the output will be written to that
file.  In this case no backup is created.
.P
If no errors occur (such as file access errors)
.I wiggle
will exit with a status of 0 if all changes were successfully merged,
and with an exit status of 1 and a brief message if any changes could
not be fully merged and were instead inserted as annotations.
However if either
.B \-\-report\-wiggles
or
.B \-\-show\-wiggles
options were given,
.I wiggle
will also exist with status of 1 if any changes had to be wiggled in
even though this was successful.
.P
The merge function can operate in three different modes with respect
to lines or words.
.P
With the
.B \-\-lines
option, whole lines are compared and any conflicts
are reported as whole lines that need to be replaced.
.P
With the
.B \-\-words
option, individual words are compared and any
conflicts are reported just covering the words affected.  This uses
the \f(CW <<<|||===>>> \fP conflict format.
.P
Without either of these options, a hybrid approach is taken.
Individual words are compared and merged, but when a conflict is found
the whole surrounding line is reported as being in conflict.
.P
.I wiggle
will ensure that every change between the two other texts is reflected
in the result of the merge somehow.  There are four different ways
that a change can be reflected.
.IP 1
If a change converts
.B A
to
.B B
and
.B A
is found at a suitable place in the original file, it is
replaced with
.BR B .
This includes the possibility that
.B B
is empty, but
not that
.B A
is empty.
.IP 2
If a change is found which simply adds
.B B
and the text immediately preceding and following the insertion are
found adjacent in the original file in a suitable place, then
.B B
is inserted between those adjacent texts.
.IP 3
If a change is found which changes
.B A
to
.B B
and this appears (based on context) to align with
.B B
in the original, then it is assumed that this change has already been
applied, and the change is ignored.  When this happens, a message
reflecting the number of ignored changes is printed by
.IR wiggle .
This optimisation can be suppressed with the
.B \-i
flag.
.IP 4
If a change is found that does not fit any of the above possibilities,
then a conflict is reported as described earlier.
.SS DIFF
The diff function is provided primarily to allow inspection of the
alignments that
.I wiggle
calculated between texts and that it uses for performing a merge.
.P
The output of the diff function is similar to the unified output of
diff.  However while diff does not output long stretches of common text,
.IR wiggle 's
diff mode outputs everything.
.P
When calculating a word-based alignment (the default),
.I wiggle
may need to show these word-based differences.  This is done using an
extension to the unified-diff format.  If a line starts with a
vertical bar, then it may contain sections surrounded by special
multi-character brackets.  The brackets "<<<++" and "++>>>" surround
added text while "<<<--" and "-->>>" surround removed text.
.P
.I wiggle
can be given the two texts to compare in one of three ways.
.P
If only one file is given, then it is treated as a patch and the two
branches of that patch are compared.  This effectively allows a patch
to be refined from a line-based patch to a word-based patch.
.P
If two files are given, then they are normally assumed to be simple
texts to be compared.
.P
If two files are given along with the \-\-patch option, then the second
file is assumed to be a patch and either the first (with \-1) or the
second (with \-2) branch is extracted and compared with text found in
the first file.
.P
This last option causes
.I wiggle
to apply a "best-fit" algorithm for aligning patch hunks with the
file before computing the differences.  This algorithm is used when
merging a patch with a file, and its value can be seen by comparing
the difference produced this way with the difference produced by first
extracting one branch of a patch into a file, and then computing the
difference of that file with the main file.
.SS EXTRACT
The extract function of
.I wiggle
simply exposes the internal functionality for extracting one branch of
a patch or a merge file.
.P
Precisely one file should be given, and it will be assumed to be a
merge file unless
.B  \-\-patch
is given, in which case a patch is assumed.
.P
The choice of branch in made by providing one of
.BR \-1 ,
.BR \-2 ,
or
.B \-3
with obvious meanings.
.SS BROWSE
The browse function of
.I wiggle
presents the result of a merge or (with
.BR \-d )
a diff in a text-based GUI that can be
navigated using keystrokes similar to
.IR vi (1)
or
.IR emacs (1).
.P
The browser allows each of the two or  three streams to be viewed individually
with colours used to highlight different sorts of text - green for
added text, red for deleted text etc.  It can also show the patch by
itself, the full result of the merge, or the merge and the patch
side-by-side.
.P
The browser provides a number of context-sensitive help pages which
can be accessed by typing '?'
.P
The top right of the GUI will report the type of text under the
cursor, which is also indicated by the colour of the text.  Options
are Unchanged, Changed, Unmatched, Extraneous, AlreadyApplied and
Conflict.  If the meanings of these are clear a little
experimentations should help.
.P
A limited amount of editing is permitted while in
.B browse
mode.  Currently text that is unwanted can be discarded with
.BR x .
This will convert a Conflict or Change to Unchanged, and an Unmatched
to Changed (which effectively changes it to the empty string).
Similarly a text can be marked as wanted with
.BR c .
This will convert a Conflict or Extraneous to Changed.  Using the same
key again will revert the change.
.P
Finally, the uppercase
.B X
will revert all changes on the current line.
.P
To make more sweeping changes you can use
.B v
which runs an editor, preferring
.B $VISUAL
or
.B $EDITOR
if they are set in the environment.
.P
If you make any changes, then wiggle will ask you if you want
to save the changes, even if
.B \-\-replace
was not given.
.SH WARNING
Caution should always be exercised when applying a rejected patch with
.IR wiggle .
When
.I patch
rejects a patch, it does so for a good reason.  Even though
.I wiggle
may be able to find a believable place to apply each textual change,
there is no guarantee that the result is correct in any semantic
sense.  The result should always be inspected to make sure it is
correct.
.SH EXAMPLES
.B "  wiggle \-\-replace file file.rej"
.br
This is the normal usage of
.I wiggle
and will take any changes in
.B file.rej
that
.I patch
could not apply, and merge them into
.BR file .
.P
.B "  wiggle \-dp1 file file.rej"
.br
This will perform a word-wise comparison between the
.B file
and the
.I before
branch of the diff in
.B file.rej
and display the differences.  This allows you to see where a given
patch would apply.
.P
.B "   wiggle \-\-merge \-\-help"
.br
Get help about the merge function of
.IR wiggle .
.P
.B "   wiggle \-\-browse \-\-patch update.patch"
.br
Parse the
.B update.patch
file for patches and present a list of patched files which can be
browsed to examine each patch in detail.
.P
.I wiggle
can be integrated with
.I git
so that it is used as the default merge tool and diff tool.
This can be achieved by adding the following lines to
.B .gitconfig
in the user's home directory.
.RS 4
.nf
[merge "wiggle"]
	name = "Wiggle flexible merging"
	driver = wiggle \-o %A %A %O %B
	recursive = binary
[merge]
	tool = wiggle
[mergetool "wiggle"]
	cmd = wiggle \-B \-o $MERGED $LOCAL $BASE $REMOTE
[difftool "wiggle"]
	cmd = wiggle \-Bd $LOCAL $REMOTE
.fi
.RE
This will make
.B "git mergetool"
and
.B "git difftool"
use
.IR wiggle .
.P
If you want
.I git
to always use
.I wiggle
for merges (which may be dangerous), you can add
.RS 4
* merge=wiggle
.RE
to an appropriate
.I gitattributes
file such as
.BR $HOME/.config/git/attributes .
.SH QUOTE
The name of
.I wiggle
was inspired by the following quote.
.P
.nf
The problem I find is that I often want to take
  (file1+patch) -> file2,
when I don't have file1.  But merge tools want to take
  (file1|file2) -> file3.
I haven't seen a graphical tool which helps you to wiggle a patch
into a file.
.br
\-\- Andrew Morton - 2002
.fi
.SH SHORTCOMINGS
.IP -
.I wiggle
cannot read the extended unified-diff output that it produces for
\-\-diff \-\-words.
.IP -
.I wiggle
cannot read the word-based merge format that it produces for \-\-merge
\-\-words.
.IP -
.I wiggle
does not understand unicode and so will treat all non-ASCII characters
much the same as it treats punctuation - it will treat each one
as a separate word.  The browser will not display non-ASCII characters
properly.
.SH AUTHOR
Neil Brown at Computer Science and Engineering at
The University of New South Wales, Sydney, Australia;
and later at SUSE, still in Sydney, Australia.
.SH SEE ALSO
.IR patch (1),
.IR diff (1),
.IR merge (1),
.IR wdiff (1),
.IR diff3 (1),
.IR git-config (1),
.IR gitattributes (5).