Configure: fixed perl Makefile generation (ticket #334).

Dependancy tracking introduced in r5169 were not handled absolute path
names properly.  Absolute names might appear in CORE_DEPS if --with-openssl
or --with-pcre configure arguments are used to build OpenSSL/PCRE
libraries.

Additionally, revert part of r5169 to set NGX_INCS from Makefile
variables.  Makefile variables have $ngx_include_opt in them, which
might result in wrong include paths being used.  As a side effect,
this also restores build with --with-http_perl_module and --without-http
at the same time.