Ensuring that site.exp no longer overrides command line options

Recently, bug#41647 was reported and I have found that it is caused by 
(1) Automake writing a relative name for srcdir into site.exp if 
configure is invoked using a relative name, (2) overriding this with a 
command-line option specifying an absolute path in the "check" recipe 
because (3) Automake invokes runtest in the "testsuite" directory but 
(4) Automake does not adjust the relative srcdir value to account for 
this, (5) site.exp overrides the command line from the time it is loaded 
until the command line is parsed for the second time, and (6) during the 
window where the command line options are overridden DejaGnu attempts to 
load the tool init file.

Obviously, this means that site.exp overriding command line options 
needs to be fixed and that window needs to be closed.  I am unsure if 
there are any uses for this "misfeature" and therefore how aggressively 
the command line parameters should be reapplied after loading the local 
init file.  Should only srcdir be restored (which should be enough to 
fix bug#41647)?  Should everything set as a result of that parse be 
stored away and restored after loading site.exp?  Should only the 
options that will be reset at the second parse be restored?  Something else?


-- Jacob