Could you upload the source code please, I'd love to build it on linux?
Also, I don't know if you know but version r5039 is already out there,
I think it would be interesting if people released updated source code from time to time with new Desmume releases,
I would be willing to do it if you teach me how to do it, just tell me what files have you changed and I'll do it.
The author of the mod updates it himself regularly. His most recent version is based of r5039 and he started to include 64 bit builds, too.
http://shikaver01.webcrow.jp/
For building it yourself on Linux you'll need TortoiseSVN or a similar tool.
Create a new folder, right click on it and select "SVN Checkout...".
In the dialog enter "
http://svn.code.sf.net/p/desmume/code/trunk" into the "URL of repository" field and click OK.
Now Tortoise will download the up to date source code.
Then you'll need the latest version of the mod from the authors page(
http://shikaver01.webcrow.jp/). The archive contains the files of the source code files, that were changed.
I'd recommend to use the .diff file though(currently DeSmuME X432R 2014-04-28-0.diff). This file can be used even if your source code is newer than the current version of the mod. Let's say you downloaded r5040 which contains changes for the file GPU.cpp. If you overwrote this file with the one from the archive, you would overwrite this changes.
The .diff file only contains the changes for the mod and can be applied to different version. Usually Tortoise will figure out how to merge the changes.
To apply the .diff file open the folder and the desmume folder inside of it. Here you have to right click on the src folder, select TortoiseSVN->Apply Patch, select the patch file and click "Patch all items".
Now you have the up to date source code with the mod.
For the Linux version you'll need to port all the changes made to the interface of DeSmuME from Windows to Linux.
To update to the latest revision, just right click the folder and select SVN Update. This won't overwrite the mod.
When the mod itself gets updated, it's easiest to just delete the whole folder and and get a fresh version.