scripts: serie_update: fixes update conflict error

Now that log console is readable, there are some errors reported.
Some are solvable with the script itself.
* ..._hal_conf_template:
  as it is renamed to ..._hal_conf.h, for zephyr as well as for
  original cube, any update is then part of global zephyr patch.
  So no need for a special treatment except for renaming.

* README, CMakeLists.txt, stm32_assert.h: all are part of the global
  So those files need to be removed before applying zephyr patch
  so that zephyr patch will recreate them
  Then only they can be updated (or regenerated)

* add a global dos2unix on the whole updated directory

Signed-off-by: Alexandre Bourdiol <alexandre.bourdiol@st.com>