The following is a picture about the interaction between Applications and JCR:
Every Content (JCR) dependent application interacts with eXo JCR via JSR-170 and eXo JCR API extension (mostly for administration) directly or using some intermediate Framework (Neither Application nor Framework should ever rely on Implementation directly!)
Content Application: all applications may use JCR as a data storage. Some of them are generic and completely decoupled from JCR API as interaction protocol hides Content storage nature (like WebDav client), some partially decoupled (like Command framework based), meaning that they do not use JCR API directly, and some (most part) use JSR-170 directly.
Frameworks is a special kind of JCR client that acts as an intermediate level between Content Repository and End Client Application. There are Protocol (WebDav, RMI or FTP servers for example) and Pattern (Command, Web(servlet), J2EE connector) specific Frameworks. It is possible to build a multi-layered (in framework sense) JCR application, for example Web application uses Web framework that uses Command framework underneath.