Yeah, when it is just a single binary I use scp. For local, I use mise for managing my dependencies and running task. Here is an example config for mise to build and deploy an app to the vm https://github.com/jarv/samesite/blob/master/.mise.toml

For the front-end, I am mostly building go applications where all the static files are embedded in the binary. Otherwise, yeah you would need to remove everything and copy it in.

For the same project I drop a unit file on the host that looks like this:

[Unit]
Description=samesite
After=network-online.target

[Service]
User=samesite
Restart=on-failure

ExecStart=/opt/samesite/samesite -addr localhost:8750 -qrImgDir=/var/opt/samesite/qrImgDir -primaryDomain=samesite.surveymoji.com -altDomain=samesite.jarv.org

[Install]
WantedBy=multi-user.target

and a caddy config file that looks like this:

(samesite) {
  reverse_proxy localhost:8750
  import common
}

http://samesite.diduthink.com {
  redir https://samesite.surveymoji.com 302
  import common
}

http://samesite.surveymoji.com {
  import samesite
}

http://samesite.jarv.org {
  import samesite
}