Edit: I successfully compiled bitcoin/master today, and here is what I learned:
In the MSYS shell, /usr and / are the same, and the folder called /usr (and /) in that shell is actually C:\MinGW\msys\1.0.
I did some simple testing:
Dave@WindowsCompiler /
$ ls
bin etc home lib m.ico msys.bat msys.ico postinstall sbin share
Dave@WindowsCompiler /
$ cd /usr
Dave@WindowsCompiler /usr
$ ls
bin etc home lib m.ico msys.bat msys.ico postinstall sbin share
Given that, I used a solution from
StackExchange:
ACLOCAL_PATH=/usr/share/aclocal ./autogen.sh
in the bitcoin directory and that avoided the PKG_... errors during the execution of ./configure.