Edit: I am mistaken, YML like syntax, but not YML

Place your custom modules somewhere outside Odoo base installation folder, for example at /opt/odoo/external_modules , and add this to /etc/openerp-server.conf:

    addons_path =  ... (base Odoo module path),/opt/odoo/external_modules

Then you can update your odoo base installation without affecting your custom modules. This will be broken if you are upgrading instead between version, e.g from V8 to V9.