My home directory is located at a separate partition. I want to install a fresh Manjaro deleting all the hidden files from home directory and keeping other files that are not related to configuration.
How can I do so?
Is that home the root directory of that partition?
I suppose yes given the thread title.
In that case, during the installation, you can use manual partitioning in order to set that partition to be mounted to /home. Beware not to format that partition!
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You don’t need to delete them right away.
mkdir ~/oldconfigs
mv ~/.* ~/oldconfigs is enough.
If needed your old stuff is then in ~/oldconfigs
Then everything goes as desired.
rm -rf ~/oldconfigs
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I think you also need to create the user with the same UID and GID, in order to access your data
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You can have a look into your /home-partition while using the USB live system (before installing). Then do like suggested here and move your config-files to a new folder.
Install Manjaro, opting for manual partitioning, binding your home-partition at /home and nnot formatting it while doing so 
The rest is the same as ever.
PS: I found that keeping the config-files for dropbox around saves you from configuring it all again - including passwords and authentification…
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