How to copy directories in OS X 10.7.3?

Is there something special with that directory or are you really just asking how to copy directories?

Copy recursively via CLI:

cp -R <sourcedir> <destdir>

If you're only seeing the files under the sourcedir being copied (instead of sourcedir as well), that's happening because you kept the trailing slash for sourcedir:

cp -R <sourcedir>/ <destdir>

The above only copies the files and their directories inside of sourcedir. Typically, you want to include the directory you're copying, so drop the trailing slash:

cp -R <sourcedir> <destdir>

tl;dr

cp -R "/src/project 1/App" "/src/project 2"

Explanation:

Using quotes will cater for spaces in the directory names

cp -R "/src/project 1/App" "/src/project 2"

If the App directory is specified in the destination directory:

cp -R "/src/project 1/App" "/src/project 2/App"

and "/src/project 2/App" already exists the result will be "/src/project 2/App/App"

Best not to specify the directory copied in the destination so that the command can be repeated over and over with the expected result.

Inside a bash script:

cp -R "${1}/App" "${2}"