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Click Tools → Filters. Or, from the Select Files or Folders dialog, click Select to the right of the Filter field. In the Filters dialog File Filters tab, click New. In the Shared or Private Filter dialog, choose Shared Filter or Private Filter (see File filter locations for their uses) and click OK.
You can begin a folder compare operation from either the WinMerge window or a Command Prompt window. Click File → Open. Use the Select Files or Folders dialog to specify the left and right folders to compare. By default, the compare includes all files in the folders, and is recursive (does include subfolders).
WinMerge handles this just fine. You want to create and use a Filter. Under Tools | Filters... | Filefilters, create a new filter or modify an existing one.
It will look like this:
## Ignore Java class and jar files
f: \.class$
f: \.jar$
## Ignore subversion housekeeping directories
d: \\.svn$
d: \\._svn$
Save it, then when selecting items to merge, select the filter you defined from the Select Files or Folders dialog box. Bonus points: It will save this and use it as a default for future merges.
WinMerge (Version 2.12.4) already includes a filter to exclude source control files and directories, and it's called Exclude Source Control.
It works for Subversion, CVS, Git, Bazaar and Mercurial, and it doesn't require you to create a filter, you just have to apply it during the comparison.
WinMerge (Version 2.12.4) already includes a filter but (at least in my installation) the filters for Subversion, Git and Bazaar were commented out.
Navigate here: Tools | Filters | Filefilters | Exclude Source Control (double click to edit)
Edit the lines to look like this:
d: \\.svn$ ## Subversion working copy
d: \\_svn$ ## Subversion working copy ASP.NET Hack
d: \\cvs$ ## CVS control directory
d: \\.git$ ## Git directory
d: \\.bzr$ ## Bazaar branch
d: \\.hg$ ## Mercurial repository
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