Squashed commit of the following:

commit 587811c804bf9723ef7745b1ed97f8510d159610
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 17:24:45 2013 -0700

    fix test, add testRepo.zip, new content

commit 77c7f88520ae6edf5d05efc8878630052ce7a1e0
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 16:12:50 2013 -0700

    use subtree merge instead of submodule

commit 96dc3921ebd90ec183d9b1a9389a29926ca78379
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 14:27:05 2013 -0700

    udate gh-pages

commit 3a8fc97d23573c9b944728258d60d10b69d56f17
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 14:09:02 2013 -0700

    update gh-pages

commit f76eab38ac4916af3a6a42532ec34434c24c28db
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 14:05:29 2013 -0700

    change theme to nature

commit bf18b297f474eff79221d80c5d782495940ed33c
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 14:02:51 2013 -0700

    add developer text

commit 916636d31f605101cec0e4621ca8a1bac015ba3e
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 14:00:48 2013 -0700

    add jgit api

commit 47519eca8ee316379a095a6455436b00566ff269
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 12:34:16 2013 -0700

    add usage/add and developers/jgit.add

commit 6f9eb2e956cf8efd7689bdbe89b8058534dbea84
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 12:20:46 2013 -0700

    add docs

commit 13ff852b254873557efe4d9ca5c9c4772467158a
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 02:26:27 2013 -0700

    add pull and push

commit 47ef022b9c1e285fcea569e23c984407f524badc
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 01:58:28 2013 -0700

    add git pull to jgit.m

commit 99a237504cce572f4d2c82c3614578aeb0cab796
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 01:50:17 2013 -0700

    add generated merge message to commit if repo state says merging resolved

commit 3a640524e7eefdb0f65bef1fe05307297c2a84b5
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 9 00:57:11 2013 -0700

    add TODO tasks, add CONFLICTING merge status

    * add check for CONFLICTING, and save *.BASE, *.LOCAL, *.REMOTE & *.orig for merge
    * reverse meld and p4m so meld is first, add note about save files, how to
    * resolve merge.

commit 25ee309ccbf01cebf70e2121a0adc129100ebb4b
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 21:14:05 2013 -0700

    list strategies, single commit, how to abort, links to merge tools

commit 0f90b5aec09481892300b4061c4007aa80e83219
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 21:12:01 2013 -0700

    add message for conflicting unmerged paths

commit 16607ebd41ce21cbbdbd3d9c6c16e9cc1a47fc95
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 20:57:45 2013 -0700

    use less space for filenames

commit c83f22ab8701b34e792fcc61d18bec77c691d0c4
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 20:56:46 2013 -0700

    add strategy, message & commit to parseMerge

commit a59458f4dcddcf90f138a9d3b262788c09d701fc
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 14:32:39 2013 -0700

    add options to parseMerge

commit 81625ae26e3045d595a3bd2dc7171cea569daf18
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 14:32:16 2013 -0700

    fix index error in assert - common problem, need to check others & make more tests

commit 96b8b437302b0cfc095a2e775a4c8f15cb1506a8
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 14:31:09 2013 -0700

    some fluff for revision ranges, clean up merge

commit 46b7b272a722730294c9c64533ee63879ee5e14e
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 14:29:49 2013 -0700

    fix bug/typo, setCommit not setSquash, ha!

commit 0269546e952fdee4f2f85538720ad3b559caaf99
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 14:25:37 2013 -0700

    no need for no-revision case, default behavior

commit 6af8099b60544df0e6b1a8cd2484c71f064091e2
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 11:50:49 2013 -0700

    add commit option to JGit.merge

commit 740e02926df4bd72cb126590e40cf69e21b61611
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 10:10:34 2013 -0700

    add RECURSIVE strategy to JGit.merge, add --all option to JGit.log, pass add/not revs as cellstrings if more than one in log, don't pass if empty

commit 1c9e09abfe8aac681f9b7645a597dea6cb971bdc
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 8 00:28:43 2013 -0700

    add all method to jgit.log, update help, add parsemerge

commit 0acae9336b7159c3d45a38ddb6edc5d299eaa1d4
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon Oct 7 14:42:15 2013 -0700

    don't show status last line for commit messages, don't call commit if no message, return gracefully instead of letting java raise no-message-exception

commit feb07b330ef913f8a7d98981a03b21c01c0bc355
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Oct 6 02:35:23 2013 -0700

    finish adding parseLog to jgit

    * fix bug didn't have p.Results.path in @JGit.checkout for paths
    * add paths as cellstr or char, add not, and add, pretty log output
    * reverse order of splitEqualSigns and splitShortOptions, can't use number
     in cell with strfunctions, hopefully no side affects of switching order
    * add parselog!
    * add options to log help
    * fix bug in parseDiff, fatal error ambiguous arg, just put in if
     statement
    * add maxCount, skip, revision range, paths, add/not keys to api
    * fix popping problem in parseOpts if hasArg
    * fix bugs in splitShortOptions wasn't handling integers correctly

commit 9024405bbebb0115f362dd976e55d15f5c8065bc
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu Oct 3 02:02:35 2013 -0700

    add parseLog

commit b03cf69f3a21a3c44361567f6eacf55008b0c625
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu Oct 3 01:52:23 2013 -0700

    add parseInit

commit f9122685297340cbf55719e0145c57578008a94a
Merge: a2342d5 0a0d360
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu Oct 3 01:23:06 2013 -0700

    Merge branch 'master' into parse_jgit

commit a2342d573517134f1b20d9201b92ae0c6a2591cf
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu Oct 3 01:22:58 2013 -0700

    add commit output message

commit 05138e1db6b0296c9307bb0f661b2f1338f28a10
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu Oct 3 00:39:47 2013 -0700

    add parseFetch and add error for trying to checkout 2 branches, ha

commit f9dfd1cad5b213383deda4046595ea3eca061adc
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 2 20:55:29 2013 -0700

    add error message if attempt to checkout path from more than one start point

commit 5bfd744e32df5cdb0b6b5e78573572da10b9851a
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 2 20:28:54 2013 -0700

    add no prefix option, fix too many hyphens in name status

commit e8e062ecfc55e1639d14c9689a60417a586374f9
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 2 17:26:53 2013 -0700

    add parseDiff

    * fix bug in download error in validate java class path in @JGit/JGit.m,
     error message must be a string, but status is an int
    * slowly updated all references from kernel.org -> git-scm.com
    * add help comments in JGit.diff that paths are actually path filters, and
     as such must be relative to GITDIR (subfolder path must be specified)
     and must use "/" to delimit folders, not windows "\" no!
    * add links to JGit path filter, tree filter and tree parser classes
    * add a hyphen between refs in diff filename
    * fix bug in JGit.diff, showNameAndStatusOnly should only ouput list to
     terminal, no stream output!
    * add diff, difftool and fetch to jgit.m
    * update filterOpts to output paths as 2nd output, not have pop input and
     separate refs from paths if 2nd output requested
    * update jgit_help.m, add aliases for branch, checkout and status, add
     diff & difftool
    * update parseCheckout to use filterOpts with 2nd arg out instead of pop
     arg in set false.
    * clean up whitespace, end all functions "end" and newline

commit a05d3df450148da97a27911b00aec9f50b3def73
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 2 12:31:58 2013 -0700

    use parseOpts in parseCommit

commit 0a0d360ae2cdf6394461271d69318aa8e68ecc37
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 2 11:52:31 2013 -0700

    add Volker to AUTHORS

commit 225789e79efde3eab2e8343ba63c3c04f6e98464
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Wed Oct 2 11:45:02 2013 -0700

    pull and close #4

commit 96ebb42774ecd155fc4889325433294169b97a1d
Author: Mark Mikofski <bwanamarko@yahoo.com>
Date:   Wed Oct 2 06:54:21 2013 -0700

    pass branch and origin args

commit 6c94d109c4876ed4450fcf535dc9c320aa7ab261
Author: Mark Mikofski <bwanamarko@yahoo.com>
Date:   Tue Oct 1 21:16:59 2013 -0700

    use parseOpts in parseClone

commit 8a4153ebed0e195d3809fefdebc4461a62b7c629
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 1 16:43:04 2013 -0700

    use new parseOpts in parseCheckout, start testCheckout

commit e87ba49993ce84e2e913d77bb6637abc82202139
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 1 15:40:10 2013 -0700

    fix bugs in JGit.commit

    * abort if no message
    * abort and show status  if no files to commit!
    * don't setName in Checkout if checking files, use tempname, very long
     random string, to set name to junk, check for path in args and check if
     name set to junk, then skip setName - have to jump through loops to make
     MATLAB inputParser happy, since it is set to look for string, and '' is
     not a string.
    * fix typo getResult singular not plural (not getResults! no!)
    * had to copy large chunk of status to check status in commit and to
     decide if there are any files to commit! Also compare modified against
     only.
    * fix bug, strtrim removes all whitespace including newline ASCII:10, this
     fix is more elegant b/c now jgit also throws java exception, we could
     catch this and only display nice abort message, but no.
    * add newline at end of non-empty message
    * in status (and commit) don't need to check ignored files, and compare to
     untracked b/c definition of untracked is already **not ignored!**
    * add different message for untracked and unstaged, don't show any message
     if neither!
    * fix missing fid, don't always print untracked to stderr, if commit is in
     editor use open file fid.
    * don't need to check for short and long options, checking for short also
     catches long options!
    * use new parseOpts in branch! yay!
    * in parseOpts change some var names: parsed_opts->options and
     options->argopts, clean up example
    * fix bug in splitShortOpts, only catch short options, ignore long options
    * add testBranch class using MATLAB unit-test framework and testRepo.zip

commit 021b57d1c78292b8b2b4792b1c7bb5805b8fc669
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 1 10:41:14 2013 -0700

    fix bugs in getUserInfo

commit a7fa349e02f1fd0c116cab326422cf8c515f9128
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 1 10:41:14 2013 -0700

    fix bugs in getUserInfo

commit 29aff0dc73fa98745701d8fc5af89f6f125b189b
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 1 03:14:02 2013 -0700

    leave argument string in cell array, easier to concatenate with other cells in parsed_args

commit 5275901cab401ba90ce183850e2f21fca02b68a0
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 1 03:09:06 2013 -0700

    pop options, and return them, scalarize option logicals

commit ffe092d2f374d02b43d3eec732a989f00aae3538
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 1 02:48:09 2013 -0700

    add splitShortOptions to separate multicommand shorties and convert ints to args

commit 94ae126de38bae37e68c1b64474babb8a11a2707
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Oct 1 01:23:47 2013 -0700

    add parseOpts

commit 4ccf5085e0cce1384c48dc15646f1fe73ba965c7
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon Sep 30 17:37:11 2013 -0700

    fix pop argopts bug index was bad

    * use | to keep indices in position, or pop when detecting, so detection
     uses new indices each time.
    * finish adding parseCOmmit
    * add splitequalsigns to remove equal signs from long options

commit bc67ce0670ebedebcea412e3a55a3bae8c726a4b
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon Sep 30 15:07:41 2013 -0700

    no it doesn't have to have an equal sign

commit 5f8a505fbb7bc10674d9db0f3a9d35e8733ff64c
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon Sep 30 15:06:41 2013 -0700

    does it have to have an equal sign

commit 571ae95168fb8382420a4dc9daf25cf6320d9a50
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon Sep 30 15:05:35 2013 -0700

    begin parsing commit, update help

commit 77016884b0d94a3b14d5977a8882aff933ce220f
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Sep 29 23:05:42 2013 -0700

    add commit help message

commit 6e9e6f898138c775e2c141d2d16e34672a6e5649
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Sep 29 23:00:52 2013 -0700

    add set only option

commit a3d0a8e1d0a1839026bbb113d154e51308e800b7
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Sep 29 21:06:58 2013 -0700

    correct help comments in clone, add parse cell in parsers, fix pop comment

commit 6608276bdcbf734099dd881a9fc4044576c1994b
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Sep 29 21:06:02 2013 -0700

    finish adding parseClone

commit b9b42669b4ae61d6938ea8d3caa3ca37fdde37b4
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Sep 29 15:06:43 2013 -0700

    fix java thinks pwd is matlab userpath, ha

commit 8bc21944c2ba75abb48209843695b29fea54a138
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Sep 29 15:08:17 2013 -0700

    add clone args, opts & help to jgit

commit d2f210f1cd08412c82b29aa3e53c271c79fb3d6c
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Sep 29 15:06:43 2013 -0700

    fix java thinks pwd is matlab userpath, ha

commit e03882efbfcb1396ae1883fefb5fee7fec51b0c8
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Sep 29 01:19:48 2013 -0700

    add ADD and CHECKOUT help, clean up, add set-update option to checkout and simplify checkout path

commit 56cc9c91d2691c42ffa53defeb3e98e06b5059b7
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Sep 29 01:16:59 2013 -0700

    cmd in alphabetical order

commit d0c7b72a68f16b5175ea16cdef2017a6c2d53373
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Sep 29 01:16:13 2013 -0700

    replace version 0.5 ... with copyright

commit 514a079b08e4be8bd8bff4cb1f0f69a8d197eff0
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat Sep 28 22:32:45 2013 -0700

    move parseCMD, filterOpts to private/

    * new style help in private/jgit_help shows synopsis consistent with man
     pages, but only available jgit commands.
    * show version and call update to download latest jar
    * show available commands for jgit help

commit c34d7ab8ead174f15642a75c16627a559a78f050
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat Sep 28 22:31:12 2013 -0700

    be consistent no >> for any code snippets

commit 2944adadf03ef1fe7778f3ef23a11841d8277590
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat Sep 28 22:30:18 2013 -0700

    remove most commonly used git commands from help, just show release once, but copyright everywhere

commit 36076c939827f65649439051464fb40884fb361b
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat Sep 28 02:27:04 2013 -0700

    fix strcmp needs any bug in checkout, change error msgid to parse*

commit a715c10487ef7d062d2985907925755f59810f20
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat Sep 28 01:39:59 2013 -0700

    add pop arg, to keep or loose dbl hyp

commit de1a5063f536f9b86a90b36bddba477df9714826
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat Sep 28 01:20:50 2013 -0700

    checkout new branch

commit 07339877564aa16b2f971ca6c03e1889db4e3519
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat Sep 28 01:07:49 2013 -0700

    start work on checkout

commit c5f90010e562e87c3065c3a962c8c57d6f7ee408
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat Sep 28 00:27:08 2013 -0700

    use filterOpts to find double-hyphen

commit e109b133f51b170fabe4554b35168d22bba7f700
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 23:46:26 2013 -0700

    send cell array of filepatterns to add if more than one

commit 97bafacc22410cc887fe9fd362587ec47e2bd259
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 23:38:20 2013 -0700

    move code to parsebranch function, always use case-sensitive str comparison

commit 2052ba4222a396633f7b83ed09cc7a4f6927ef81
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 21:59:56 2013 -0700

    remove +++ for H3

commit bb9830d030814c6310eb97da18e46842336bab06
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 21:59:56 2013 -0700

    remove +++ for H3

commit d9dfd57dcda84fc06b123d847fc1ab49f3a3a012
Merge: 62bf98a 7198a71
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 21:18:09 2013 -0700

    Merge branch 'master' into parse_jgit

commit 7198a71d11824bda736a4be62011d5972163431f
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 21:17:46 2013 -0700

    update README

commit 62bf98a8feb796df78ed39aa79b28ec235b0d0f2
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 18:10:17 2013 -0700

    help outside switch-case

commit fc1e28c895de29cc341eb0f8e03ef51a108bc8d9
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 18:07:39 2013 -0700

    fix bugs

commit 486bbb5bf3a4ce3e930e5f88c5f45ec05a41627e
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 17:46:58 2013 -0700

    listmode

commit 4804f8fc5f11acb5cb4c4406c5d3bcbb170670f4
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 17:37:01 2013 -0700

    branch delete

commit d3f15f3e86719425963dc97e53b7c624dc2ee6f1
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 17:29:11 2013 -0700

    add branch rename

commit f968c12b2bef7bf3867f63f6d3db2779d78f8fea
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 17:17:45 2013 -0700

    add add, branch-create

commit c03acac6d0363e2e09c02b13d73706d2c854533b
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 16:41:17 2013 -0700

    doing brute force, still stuck in parser mindset tho

commit 1dd9b3583bde102c6bb01a719babd20b3d2d7809
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 15:56:41 2013 -0700

    use GRAMMAR & argparse or bruteforce?

commit ea6f13204381aac7e1e43d479709bb1957601111
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 14:00:46 2013 -0700

    update see also's, add fetch to JGit, push uses "remote", not "setRemote"!

commit b6b84b0b3ab212645442e28f7dd5c3c1624665a9
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 13:54:37 2013 -0700

    add fetch

commit c0c70500e7b9ed21bf71ad1b0506ec721546def3
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 13:22:27 2013 -0700

    add pull, set return for pull, output mergestatus for pull/merge

commit ebae829830e39e2f24ef14a4e26c87bfffa753dc
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 12:50:02 2013 -0700

    add setRefSpecs to push

    * send strings as ArrayList too

commit 6045b7716f48f2253f4ee93cbc16cbea5f6a62f8
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 12:16:23 2013 -0700

    fix format errors, clean up first time message, use rethrow

commit 84a720c63a8a4a78a56c682c6bc5432d866a23e5
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 11:53:56 2013 -0700

    add to first time message to set user name and email.

commit ded8ebb632b1ea9915469a5048f3b1960781ae02
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 11:48:51 2013 -0700

    update MATLABPROGRESSMONITOR constant with shorter jar-file names

    * add comments why MATLABProgressMonitor and UserInfoSshSessionFactory
    are needed.
    * Check for UserInfoSshSessionFactory.jar in "javaclasspath.txt"
    * write UserInfoSshSessionFactory.jar path in new javaclasspath.txt
    * add UserInfoSshSessionFactory.jar path in existing javaclasspath.txt
    * Add first time message to set up SSH keys with link to putty gen.
    * add warnings for missing user info
    * add warning for missing ssh passphrase
    * wrap long lines
    * use char to conver java.io.File to MATLAB char

commit e3cd29e5de222f41722996c34351036f44e3f617
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 11:41:17 2013 -0700

    add example for commit message with quotes and add example that does not work

commit 4fd8688cc3b5b4ea8be9a0bb42a60153a9c42653
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 11:40:02 2013 -0700

    do not display SshSessionFactory instance, add nice comment

commit 973314207bd9c7f9bbbaca9d75bfd30b721c2d5f
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 11:23:09 2013 -0700

    ignore png files

commit 4ee93224c7b42444e93338b49a74b00d4148d014
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 10:30:34 2013 -0700

    fix relative paths for init/clone

commit e1683d8e247cb72ffc298385e30c69e7332bd79b
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 10:28:40 2013 -0700

    add config.load to get/set user info

commit 061694812c7d0e53530db968341fde65eb196c29
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 05:22:26 2013 -0700

    fix signature for push, ref is optional

commit 75f4cc44fa3c70cf90a159fc073c04deb4af8879
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 05:21:25 2013 -0700

    fix java always clones to MATLAB working dir with rel path, add passphrase setter

commit 88ec56c978495b6365004c2d0b643bf22ecb615f
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 04:45:32 2013 -0700

    finish push cmd

commit 6dea3f0567befe5d5892c96183aa95db74f490e9
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 04:37:14 2013 -0700

    JscConfigSessionFactory must be instantiated, not subclassed

commit b49c4cd5ce7fa2ee2277d670c7da9957de798728
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 04:21:32 2013 -0700

    ignore jsch

commit c5c082731d57e0deaac48825833a6d8b812588c8
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 04:20:50 2013 -0700

    ignore git merge *.orig

commit 7252e6256280212d61a1681e61f51f67946ae602
Merge: 5a792d8 0501d0c
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 04:19:27 2013 -0700

    Merge branch 'master' of github.com:mikofski/JGit4MATLAB

    Conflicts:
    	@JGit/JGit.m

commit 5a792d85a3334f50a77c3b7f9fd22342cb41d9f8
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 04:15:45 2013 -0700

    add JscConfigSessionFactory, fix broken MATLABProgressMonitor

commit cc014ce931914d770a8ca221f90d37749e2d514d
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 01:46:47 2013 -0700

    rename MATLABProgressMonitor to com.mikofski.jgit4matlab

commit 0501d0ce064568e2dca121166b28b25c3e422389
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Fri Sep 27 01:41:55 2013 -0700

    use stdout, fix download, classpath bugs

commit 092e3f21c49d91eb84b7192736b5a334e9cd1b6b
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu Sep 26 02:00:31 2013 -0700

    ignore old versions folder

commit f3b45c71fdce304a5b3872e99391e1befb143c47
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu Sep 26 01:57:46 2013 -0700

    update download link, backup old versions

commit 9fb39a0b7f92bb9bc59612ff70bb158cafb86f16
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Sep 17 12:42:17 2013 -0700

    ignore version

commit 2eec5f74b94c22d74054685c6b050b6c329e675c
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Jun 4 16:30:05 2013 -0700

    add merge, update to release 0.4, fix results out bug

commit fad9663b23d59332fd5387ba6f506c54167a6707
Merge: 7ed865a 767d6d4
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Jun 4 14:41:45 2013 -0700

    Merge branch 'master' of github.com:mikofski/JGit4MATLAB

commit 7ed865abb19d4722298be67fd05cff175c24874e
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Jun 4 14:41:29 2013 -0700

    replace colon with period as file sep, abbrev SHA to 8 digits, enclose in brackets

commit 767d6d40a370146fb09fec6546b4ff7116858419
Author: Mark Mikofski <bwana.marko@yahoo.com>
Date:   Wed May 29 10:16:38 2013 -0600

    Create license.txt

    add bsd 2-clause license from matlab fex

commit 2490cc499c71f92cf2cbb23a4b7f2b7bd6450e5a
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu May 23 11:01:55 2013 -0700

    fix bug in diff, replace path separator slash with colon

    * fix jgit CLI tool, replace string bools and numbers with bools and numbers

commit 414c33e882fa1b0b9e72c77973db22d3dfc80f9e
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu May 23 10:25:19 2013 -0700

    fix no arg call

commit dc5d9ebc615963fa60a2aa7b210df51a9cd934e7
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu May 23 10:13:47 2013 -0700

    a commandline tool for calling static JGit classes

commit 9b97f64762d3453a88ca057792a4716ac4ac7957
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Thu May 23 09:39:19 2013 -0700

    ignore jgit.misc

commit b1b3559cb60d5286dd6785a1aa65bbcb815f96bc
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue May 14 11:14:46 2013 -0700

    add jgit.diff

    * fix typo in git checkout, getResults should be boolean
    * new diff method diffs files and staged files, will use MATLAB visual
    * comparison tool if difftool is true

commit 6a4b5d1dc49a31eb5b6d88037ad4b874d7bb64b0
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon May 6 01:11:35 2013 -0700

    only add paths if not empty!

commit 808af58ea4fea026162f85a10c52a927283111b4
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon May 6 01:09:09 2013 -0700

    add checkout signature

commit 36c5094a772935c6949bf73875e6817e20461237
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon May 6 01:07:01 2013 -0700

    add checkout

commit 51158f0333620be2ad87e697e95c517efe2e2895
Merge: 9855cc8 3b7e1ec
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat May 4 21:20:10 2013 -0700

    Merge branch 'master' into gitCheckout

commit 9855cc8ebe4ad3e8672e40ac20da2e0e5f942176
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat May 4 21:20:05 2013 -0700

    ignore .zip

commit 3b7e1eccca8b1218155eb93955e8d22d019606b3
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sat May 4 21:16:55 2013 -0700

    fix H1 line in clone, better H1 in init.

commit cc43865178125a200897d76dc1b6121576b714f9
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 23 15:18:55 2013 -0700

    remove comments about javaArray, passing args to Java and handling returns

commit d70a3543501a8fc99b31370c88a566b2e5626789
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 23 15:10:10 2013 -0700

    add branch

    * rev up to Chameleon (0.3)
    * branch has 2 required inputs, cmd & newName - change in signature
    * fix validator for files in add was using "files" not "x"
    * refactor validatefiles to remove return and always set tf
    * branchesToClone default is master
    * directory default is "uriish.humanish" which is whatever jgit thinks
     repo should be named
    * fix example in clone was for log!
    * remove uri from PARAMETER,VALUE pairs, since it is listed as required
     first

commit ba881d344c4019be644f8aa2fac89ec65e9a649e
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 23 09:06:31 2013 -0700

    finish adding all clone options

commit 501bda630a86c84ef458702cbf5a8ab1a5f43e60
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 23 03:48:21 2013 -0700

    add MATLABProgressMonitor

    * java and jar file to display clone progress for MATLAB on PC, which
     doesn't display \r
    * add constant PROGRESSMONITOR =
    	 org.eclipse.jgit.lib.MATLABProgressMonitor
    * change pathlist to files for add signature
    * add branch signature
    * clone signature needs uri, which is required input arg
    * add pmjar and checks for pmjar in @JGit/ and also in class path
    * refactor search for jgitjar and pmjar so that both can be search in
     single pass of classpath
    * add some missing semicolons, even on Java commands, suppress output
    * MATLABProgressMonitor, add numChar member, and loop over adding
     backspaces, \b, except for endtask, then add newline, also change from
     System.err to System.out
    * add clone

commit d1d47a703ee94149eb8afb8b97c6fa5394475d14
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon Apr 22 21:23:33 2013 -0700

    add all command help, rev up to bumblebee, simplify JGit help

commit 8925411b34c8a7ce08a18edc1e6384225241836a
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon Apr 22 19:29:42 2013 -0700

    use files instead of pathlist

commit 4cc899382657e91dbf72bd22bb35b4559b122627
Merge: 0d69b5f cb48bba
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon Apr 22 16:42:19 2013 -0700

    Merge branch 'master' of github.com:mikofski/JGit4MATLAB

commit 0d69b5fce713d6e7e68331b98c1c4640ba8929e0
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon Apr 22 16:41:49 2013 -0700

    add the init command to initialize git repo

    * add 'update' option to add command
    * update JGit help comments with add('update') and init
    * replace 'notepad' EDITOR with getEDITOR which checks system type and assigns correct default system editor, mac=textedit, linux=gedit
    * add some comments to constant properties
    * add VALID property, checks if javaclasspath and jar package are valid - this makes it easier to install JGit, and only checks the classpath once, when JGit is instantiated - also matches install directions.
    * add VERSION and VERFILE a text file with version number - so using downloadJGitJar can be used to update JGit if out of date
    * remove validation getGitAPI to validateJavaclasspath which is more appropriate
    * fix all error identifiers to start with "jgit" not git!
    * add at least the first line of help for each function
    * fix validateJavaClassPath to return error message if not valid by using if-else-end instead of return.
    * print version to file in downloadJGitJar
    * new getEDITOR function
    * add help to add command
    * use inputparser and add update option
    * create addCMD, add all files first then call addCMD.call, not each loop!
    * create custom validator for pathlist
    * add help to commit, comments and code cell titles
    * don't return git or anything from any functions!
    * fix java.lang.String needs char, need newline and need class for constant property
    * add trailing end for log
    * add version file, easiest if this already exists, so just include it in repo and deploy

commit 9d459b32a0b194d1b3d0d4f7d88073d08977dabe
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Sun Apr 21 23:16:17 2013 -0700

    add init.m

    * add function signatures for init and clone
    * in log, delete the reply, if there is one, in addition to the prompt

commit cb48bba3e3550d7b7e946909235670634edf1280
Author: Mark Mikofski <bwanamarko@yahoo.com>
Date:   Thu Apr 18 10:56:33 2013 -0700

    add log usage and TODO

commit 25e18abe2e06a0c196702d3e38d1c6b02d89566e
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 22:05:51 2013 -0700

    improve log, add strtrim to commit, more help

    * use fprintf in log instead of disp
    * add meaningfull text to prompt, and delete it after response
    * use strtrim to cleanup commit messages
    * add log parameters and status arguments to help
    * add help for getGitDir

commit a5077c746ec34897c403c16edd82425a581fdb03
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 21:24:08 2013 -0700

    improve help

commit 072add3d409c5ffc09430e7ce6dd5a5b8b2fe56a
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 16:58:52 2013 -0700

    add log function

    * use `add()` instead of `all()` since it has problems with peeled tags
    * see https://bugs.eclipse.org/bugs/show_bug.cgi?id=402025

commit 2c3d1ec081d74a414dbc5d921211d2afa2faf298
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 13:17:57 2013 -0700

    fix code in README

commit 288e9ff7efb8de3c5db62a49beea9467e53e4c3a
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 13:10:33 2013 -0700

    fix README, copy javaclasspath before altering

commit 5986d71578addd7e6ba1a33b43a74039b8227da7
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 12:58:32 2013 -0700

    ignore org.eclipse.jgit.jar

    * fix on java class path but not downloaded bug
    * fix fresh downloaded should be invalid - requires restart
    * add .gitignore
    * change "status" to "valid" - "status" already used by downloadJGitJar
    * pass filename to downloadJGitJar, always downloads to same folder as class path
    * fix is ignored and untracked shouldn't show in status

commit e051d0147ce49b776410690a4f500ad4f2e068af
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 12:19:38 2013 -0700

    add README

commit f5841723afeca98c0620fc1936eb8df4d005fd64
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 12:03:36 2013 -0700

    abort commit if empty message in editor

    * align deleted with other status messages

commit abab369e687378a2e1be4513bea04cb31e008751
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 11:56:16 2013 -0700

    break out commands to separate files

    * change git to JGit and use @JGit folder

commit d7a5c93e38978202471b010ea5251ed319990450
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 11:17:16 2013 -0700

    supress Java output from --all and --message

commit 8fb5f7f715f961ce200cb9d84abd526e9115047d
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 11:15:45 2013 -0700

    improve validateJavaClassPath

commit 649c591ba4eb6c5e7f08c99d4bfc8996f55c7a80
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 10:34:08 2013 -0700

    fix amend bug

commit 4809e1c0fde810ebfaa51721a46092156686b351
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Tue Apr 16 10:33:03 2013 -0700

    import git commit --amend

    * add text: "initial commit" inside status message in editor
    * add amended commit message at top of editor

commit 3521d8f19b9a60705d59c2d9563ed38798909711
Author: Mark Mikofski <mark.mikofski@sunpowercorp.com>
Date:   Mon Apr 15 21:59:21 2013 -0700

    add "add" and "commit"

    * amended to remove comments