Putting plugin files into the theme is not recommend, quite the contrary.

If you really have to change the plugin, create a Git repository for the plugin directory:

cd plugindirectory
git init

Now create a new branch:

git checkout -b modified

Git will now hold the original state in the branch master and you can edit the files in the branch modified.

When there is an update for the original available, you switch to the master …

git checkout master

… run the update, make a commit …

git add .
git commit -m 'update'

and then merge the improvements into your modifications:

git checkout modified
git merge master

You can automate these tasks and run the git commands per script on updates.

Keep your theme directory as clean as possible and the plugin code “updatable”.

Putting plugin files into the theme is not recommend, quite the contrary.

If you really have to change the plugin, create a Git repository for the plugin directory:

cd plugindirectory
git init

Now create a new branch:

git checkout -b modified

Git will now hold the original state in the branch master and you can edit the files in the branch modified.

When there is an update for the original available, you switch to the master …

git checkout master

… run the update, make a commit …

git add .
git commit -m 'update'

and then merge the improvements into your modifications:

git checkout modified
git merge master

You can automate these tasks and run the git commands per script on updates.

Keep your theme directory as clean as possible and the plugin code “updatable”.