Pfthb

Below is the tree of each branch I have in a git repo

[branch1]
+ boot
 - cmdline.txt
 - config.txt
+ etc
 - fstab

[branch2]
+ etc
 - passwd
 - shadow
 - group

when I checkout branch2, files from branch1 are being removed from worktree and vice versa. How to checkout a branch without removing the exclusive files from the current branch?

It's a normal feature.

You have to add your files and commit your initial branch:

git add .
git commit -m "hello dev of branch 1"

to go to next branch:

git checkout branch2

And merge your branch1 to branch2:

git merge branch1

There isn't an easy way to do what you're describing, because it runs against the grain of git branches.

Branches in git are meant for tracking different lines of evolution of the same content. This isn't to say that it's the only possible use - git is very flexible - but that is the intent, and anything else may or may not be easy to do.

And in particular, switching back and forth between branches that contain different content, to keep the combined content on the work tree, is not something that's easy to do[1].

I recommend you take a step back and look at why you want one branch to have the password files, and another branch to have the boot directory and fstab. Understanding what problem you're trying to solve there, we might be able to suggest an alternative solution to that problem so that you can use git more in tune with its design.

At a bare minimum, to make what you're doing "work" (and I put "work" in quotes, because it's likely to have some quirky side-effects), you would probably want to:

• On each branch, add the files excluded from that branch to .gitignore
  


• Before switching to a branch that includes files not on the current branch, you may have to remove the working copies of those files. (In the simple two-branch example, you might do this with git clean -x, but be aware this would also sweep up any other ignored working tree files - such as build artifacts that would then have to be regenerated.)


• After switching to a branch that excludes files on the current branch, check those files out from the current branch (git checkout HEAD@1 -- ets/fstab and so on)

Honestly that doesn't sound like much fun for a "might work basically correctly most of the time" solution, which is why I recommend instead looking at why you have different files on different branches.

[1] That may seem weird, if you are used to tools that do use branches in that way. But if you look at the general case of branches as defined by git, you will realize there are good reasons why it doesn't want to make assumptions that would make this "easy".

Understand how Git works!

By default, every Git branch has an ancestor except the initial master branch which is an ancestor to all other branches. So if any branch has only exclusive files than any other branch then you should have deleted all the files from the branch initially and added some exclusive files to it.

So if the branch1 is an ancestor to branch2 and branch2 don't have the files of branch1 then branch2 is marked to not contain files of branch1. So merging branch1 to branch2 will remove the files of branch1 in branch2. Yes, merging an ancestor has no effect other than updating the changes of the ancestor.

Though one can git checkout --orphan NewOrphan, It can't be merged with another branch with a different history (ancestor).

So the only way to do it is as @EugenConstantinDinca said in the comment. Or rethink what you are trying to achieve by not removing the files of the parent branch.