devtool/upgrade: correctly handle recipes where S is a subdir of upstream tree

'devtool modify' writes additional settings to workspace .bbappend so that this
can be handled correctly, but 'devtool upgrade' does not. This adds the missing
settings.

In particular, local files should not anymore mysteriously disappear from
SRC_URIs on upgrades.

Signed-off-by: Alexander Kanavin <alex@linutronix.de>
Signed-off-by: Alexandre Belloni <alexandre.belloni@bootlin.com>