You can’t directly, as the corresponding desktop specification files are part of the OSTree Deployment, which is read-only.
However, you can hide it. Example for Youtube:
Get the current Deployment:
ostree admin status
will give you something like:
* eos 964fe05939b539b6273b6e44a52e179e91f86fa64cbca44bc7ed32c38d094018.0
Version: 3.9.1
origin refspec: eos:os/eos/amd64/eos3a
GPG: Signature made Mon 07 Dec 2020 04:33:36 PM CET using RSA key ID 9E08D8DABA02FC46
GPG: Good signature from "EOS OSTree Signing Key 1 <maintainers@endlessm.com>"
GPG: Key expires Sat 30 Jun 2029 06:18:11 PM CEST
GPG: Signature made Mon 07 Dec 2020 04:33:40 PM CET using RSA key ID FCF17B17F1F8E157
GPG: Good signature from "EOS Flatpak Signing Key 1 <maintainers@endlessm.com>"
GPG: Key expires Tue 09 Jun 2026 07:47:38 PM CEST
eos dbc65bfff121b358e77af3f84fa870037a5f5ba7a7b1b47dcc49a4ffc413a28f.0 (rollback)
Version: 3.9.0
origin refspec: eos:os/eos/amd64/eos3a
GPG: Signature made Mon 09 Nov 2020 04:34:41 PM CET using RSA key ID 9E08D8DABA02FC46
GPG: Good signature from "EOS OSTree Signing Key 1 <maintainers@endlessm.com>"
GPG: Key expires Sat 30 Jun 2029 06:18:11 PM CEST
GPG: Signature made Mon 09 Nov 2020 04:34:45 PM CET using RSA key ID FCF17B17F1F8E157
GPG: Good signature from "EOS Flatpak Signing Key 1 <maintainers@endlessm.com>"
GPG: Key expires Tue 09 Jun 2026 07:47:38 PM CEST
The currently booted deployment is marked with a asterix. Remember the Hash for the deployment, in my case 964fe05939b539b6273b6e44a52e179e91f86fa64cbca44bc7ed32c38d094018.0.
Find the corresponding Desktop specification
All the Specification files are located under the following Path:
/sysroot/ostree/deploy/eos/deploy/964fe05939b539b6273b6e44a52e179e91f86fa64cbca44bc7ed32c38d094018.0/usr/share/applications
(Replace the Hash with yours from the first Step).
Now, copy the file - eos-link-youtube.desktop in this case - to your local path ~/.local/share/applications
Hide the Entry
Edit the file in your local path with the Editor and insert the following line:
Hidden=true
Now the entry no longer shows up.
Probably a better solution is to simply keep everything you use on a daily basis on the first page of the Desktop and everything else from the second one onward.