libtool flags and "extern"

[JRBCAST]

Hi,

I am porting an existing library to make it gnu compliant by using
autotools. For building libraries I am using libtool but I am facing a
problem when trying to link some programs against those libraries with
undefined references. I have located the problem during compiling stage
(When generating objects for the libraries). Before it was done :

g++ -o foo.o -I/usr/include -fPIC foo.cc -c

And now with autotools it does:

g++ -I/includes -g -O2 -c foo.cc -MT foo.lo -MD -MP -MF .deps/foo.TPlo
-o foo.o

The problem is that I can not find what do those flags mean and why are
they causing problems. 

Libraries are built OK and problems are only with files newly added
which use "extern" functions... Do you know about issues with externs?

Thanks very much