You should be fine as long as you are not using formtools or attempting to use the FarCry jQuery/Bootstrap libraries that ship with core.
We spent some considerable time isolating FarCry Bootstrap/jQuery from project based libraries. The webtop, containers and FarCry tray are all Bootstrap 2.3.2 and they have their own jQuery namespace at fc-.
If you are simply using skin:loadJS to load jquery you will end up loading FarCry’s own jQuery fc-jquery, including functions for the FarCry tray. Bootstrap 3 will need it’s own copy of jQuery. Use registerJS to register your own jquery library for use in the front end.
<!-- /yourproject/config/_serverSpecificVarsAfterInit.cfm -->
<skin:registerJS id="jquery" baseHREF="/js" lFiles="jquery.min.js" />
Also check the docs for skin:registerJS and skin:loadjs
FarCry will detect that you have loaded a separate library and load its own fc-jquery as needed.
Chelsea is Bootstrap 2.3.2 – you can review the original HTML/CSS design at its GitHub repo.