I have a command that I need to run in java along these lines:
C:\\path\\that has\\spaces\\plink -arg1 foo -arg2 bar \"path/on/remote/machine/iperf -arg3
Each argument you pass to the command should be a separate String element.
So you command array should look more like...
String[] a = new String[] {
"C:\path\that has\spaces\plink",
"-arg1",
"foo",
"-arg2",
"bar",
"path/on/remote/machine/iperf -arg3 hello -arg4 world"};
Each element will now appear as a individual element in the programs args
variable
I would also, greatly, encourage you to use ProcessBuilder instead, as it is easier to configure and doesn't require you to wrap some commands in "\"...\""