You should never have to add these entries manually. You only add confusion with this and you mask the underlying problem.
I just googled your actual issue: "Cannot determine the location of the VS Common Tools folder."
This question shows the potential problems for VS2010, but it's the same thing for VS2015:
The error occurs in C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\bin\vcvars32.bat (which initializes the VS Command Prompt) and it has nothing to do with our tools.
You can open the shortcut in Start Menu\Programs\Visual Studio 2015\Visual Studio Tools\Windows Desktop Command Prompts\VS2015 x86 Native Tools Command Prompt
and you should get the same error message.
If you can fix this error, then our tools should also work fine (waf uses the same VS Command Prompt to determine the correct configuration).
I think you should read the suggestions at the StackOverflow question, there could be many issues behind this.
The first thing to check is the following registry key (just open a Windows Command Prompt and type this command):
reg query "HKLM\SOFTWARE\Wow6432Node\Microsoft\VisualStudio\SxS\VS7" /v "14.0"
You should get the following output if the registry key is correct:
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\VisualStudio\SxS\VS7
14.0 REG_SZ C:\Program Files (x86)\Microsoft Visual Studio 14.0\
If you don't get this value, then you can add/modify it manually using regedit.
vcvars32.bat runs the same command to find the VS Common Tools folder, so you can fix all your problems if you can make this work.