There are many ways to have fun with Perl + Inline::C. I chose to separate the Perl and C source files. In fact, created Sandboxing with Perl + MCE + Inline::C some time back. The algorithm3.pl script works out of the box. The other two scripts require dependencies mentioned in the README file.

./bin/
  algorithm3.pl
  primesieve.pl
  primeutil.pl

./src
  algorithm3.c
  bits.h
  output.h
  sandbox.h
  sprintull.h
  typemap
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The following is the Inline::C bits inside algorithm3.pl. I chose to hide the .Inline directory under the base dir.

BEGIN {
   $ENV{PERL_INLINE_DIRECTORY} = "${base_dir}/.Inline";
   mkdir "${base_dir}/.Inline" unless -d "${base_dir}/.Inline";
}

use Inline 'C' => Config =>
   CCFLAGSEX => "-I${base_dir}/src -O2 -fsigned-char -fomit-frame-poin
+ter",
   TYPEMAPS => "${base_dir}/src/typemap";

use Inline 'C' => "${base_dir}/src/algorithm3.c";
[download]

Well, this may not be a perfect solution. I am still learning Inline::C.