git - CRLF issue in windows + linux dual boot

I'm going to answer my question with the fix what solved my problem.

Note for downvoters: I understand that the root cause is discussed in various other threads (that is how I solved my problem). This post is more about how having a dual boot system can lead you to this issue. So no, this question/answer is not a duplicate, but a particular instance of a general class of problems, adding more cases to SO's repository on this issue.

At home: I code in Linux. LF used as line ending
At the office: I code in windows. CRLF used as line endings.
By default, git's autocrlf feature (https://stackoverflow.com/a/20653073/2715083) keeps things happy.

However, if you run a dual boot system with Linux and Windows, you can mess yourself up in the following way:

1. git pull some files you worked on in a linux environment in a windows environment, in a location that can be accessed from the dual-booted linux environment. This modifies the files to contain CRLF endings.
2. Then when you open up the file in linux, where the default is only LF, git diff will say entire file is modified, because each LF got changed to CRLF at every single line. (I was warned by Atom, which has this diff count inbuilt)