# create a new module skeleton:
$ h2xs -AXn My::App
...
$ cd My-App

# remove unused lib directory and the module skeleton inside
$ rm -Rf lib

# create dirs for binaries and documentation
$ mkdir bin
$ mkdir pod

# and move your files there
$ mv .../my-scripts.pl bin
$ mv .../my-docs.pod pod

# recreate the MANIFEST
$ rm MANIFEST
$ perl Makefile.PL
$ make manifest

# and update the Makefile.PL to install the scripts
# and manual pages automatically:
$ vi Makefile.PL