1) Is it possible to do an
in-place migration, while keeping all data in HDFS safely?
yes. stop the HDFS firstly, then run "start-dfs.sh -upgrade"
2) If it is yes, is there any doc/guidance to do this?
you just want a HDFS upgrade, so I dont think there are some useful doc.
3) Is the 2.0.3 MR API binary compatible with the one of 1.0.1?
Not much compatible of the FileSystem API. and there are some new HDFS configurations and some deprecates.