Read the remainder of the process output so that it will exit

[gdgib-roche]

Without this addition...

• IF the apt command has a lot of output (happens with proprietary, non-public packages)
• THEN the apt command may fill it's standard output buffer, and hang waiting for buffer space
• This results in the waitFor() call on line 213 (216 after this change) to never return, since apt is waiting for this very code to empty the buffer

Proposed (and tested) solution: simply empty the buffer as is commonly required when using process builder.

Technically we should do the same for stderr, but I had a hard time imagining it dumping that much to stderr and wanted to keep this change small