Process nix.conf options in "new" nix commands, add test.

Without this (minor) change, the options set using "--option"
or read from nix.conf were parsed but not used.

src/nix/main.cc

@@ -42,6 +42,7 @@ void mainWrapped(int argc, char * * argv)
     NixArgs args;
 
     args.parseCmdline(argvToStrings(argc, argv));
+    settings.update();
 
     assert(args.command);
 

tests/timeout.sh

@@ -29,3 +29,8 @@ if nix-build timeout.nix -A closeLog; then
     echo "build should have failed"
     exit 1
 fi
+
+if nix build -f timeout.nix silent --option build-max-silent-time 2; then
+    echo "build should have failed"
+    exit 1
+fi