Set R_set_command_line_arguments() to reflect what actually happens

[DavisVaughan]

Some packages like startup::startup() utilize commandArgs() to make decisions. For example, that package checks to see if --no-site-file is in the list of command args. If it is, then it refuses to try and load the "extended" site profiles that that package specially supports. Same with --no-init-file.

The problem is that we "manually" run both .Rprofile.site and .Rprofile for the user once ark has set up enough to be able to handle running arbitrary scripts. We have to forcibly tell R not to run these by setting --no-site-file and --no-init-file, even if we eventually run them. This confuses the startup package.

We should probably retain a copy of args that reflect the "real" state of the world and call R_set_command_line_arguments() after calling Rf_initialize_R() with the "fake" args. This is what commandArgs() ends up pulling from.

A test plan for this would be an integration test that checks commandArgs() after startup with a test client that allows both the user and site level R profiles to run. The command args should not contain --no-site-file nor --no-init-file