First you will need to obtain the dependencies for compiling dolphin. Even if you've built a previous version of dolphin, there are new dependencies
Ubuntu look here Everyone else look here
You will need to check your GNU compiler version, with the terminal command
gcc --version
It needs to be atleast 4.9.1, if it is not you will need to update it. For Ubuntu 14.04 and Mint 17 follow this GUIDE
Now once the legwork is completed you will need to follow these steps in terminal
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git checkout be9416c462b1b5f0074d8a3a2b35171f2a154693
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cd dolphin
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mkdir build
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cd build
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cmake ../
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make -j5 (The number after j is cpu core count + 1)
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sudo make install (Will not work if you do not install, you can change its name later)
Now to rename our newly built and installed dolphin. (If you use no other versions of dolphin, don't bother with these steps)
sudo cp /usr/local/bin/dolphin-emu /usr/bin/dolphin-nand
sudo rm /usr/local/bin/dolphin-emu
sudo rm /usr/local/bin/dolphin-emu-nogui
sudo cp /usr/local/share/applications/dolphin-emu.desktop /usr/local/share/applications/dolphin-7161.desktop
sudo gedit /usr/local/share/applications/dolphin-7161.desktop (then edit the name to whatever you want and change the exec to dolphin-7161, change the icon too if you're so inclined)
sudo rm /usr/local/share/applications/dolphin-emu.desktop
And now you should have a menu option for Dolphin5.0-321 and be able to install whatever other copy of dolphin master you'd like to be using.
Troubleshooting:
Launching games fails with "WriteRest Op" error
Add "-fno-pie" to "CXX_FLAGS" when building Dolphin.
Launching Wii games in Netplay fails with "Invalid SYSCONF" error
This is why I told you to sudo make install
cxx compiler identification is unknown
make sure you have g++ installed