What are some alternatives to WinMerge and the pros and cons of each?
3 Answers
The best I like is Meld
There are many choices available though. As a vim fan I find myself using vimdiff, kompare for the kde crowd - there also some paid version that have linux versions like Beyond Compare . The pros/cons depends on what you're looking for/looking to do.
vimdiff is great because you can run it from a terminal, over an ssh connection, and if you already use vim, you get to keep your tools/config options.
Meld has a pretty clean user interface, and does three way and directory diffs. You'll have to try a couple and see which does the job as you're expecting them to do for your own needs.
To install Meld
from the Ubuntu repos, you can run:
sudo apt-get install meld
You can then pick the files/folders to compare, and compare them:

Kdiff3
Is a pretty good 3 way merge tool.

Some of its features are:
- compares or merges two or three text input files or directories,
- shows the differences line by line and character by character (!),
- provides an automatic merge-facility and
- an integrated editor for comfortable solving of merge-conflicts,
- supports Unicode, UTF-8 and other codecs, autodetection via byte-order-mark "BOM"
- supports KIO on KDE (allows accessing ftp, sftp, fish, smb etc.),
- Printing of differences,
- Manual alignment of lines,
- Automatic merging of version control history ($Log$),
- and has an intuitive graphical user interface.
- Windows-Explorer integration Diff-Ext-for-KDiff3 - shell extension included in installer
KDE-Konqueror service menu plugin
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