atmel_sam3: Do not switch off CPU clock if debugging is planned

at91sam3 supposed to go to Sleep mode and stop the CPU clock
(HCLK). It leads to JTAG problems. In order to be able to use
JTAG, we need to keep CPU clock on. This is achieved by
switching to Wait mode and keeping external main clock.
Since Wait mode switches off automatically Fast RC Oscillator,
but keeps external clock untouched.

Change-Id: Ife37a7691c3cbdf434e560725a71d419adafe054
Signed-off-by: Dmitriy Korovkin <dmitriy.korovkin@windriver.com>