refactor initialization for embedded api

.gitignore

...fle.r.engine/src/com/oracle/truffle/r/engine/REngine.java

...ngine/src/com/oracle/truffle/r/engine/shell/RCommand.java

...gine/src/com/oracle/truffle/r/engine/shell/REmbedded.java

...e/src/com/oracle/truffle/r/engine/shell/RStartParams.java

...src/com/oracle/truffle/r/engine/shell/RscriptCommand.java

...racle.truffle.r.native/fficall/src/common/unimplemented.c

com.oracle.truffle.r.native/fficall/src/jni/Rembedded.c

...e/truffle/r/nodes/builtin/base/CapabilitiesFunctions.java

.../com/oracle/truffle/r/nodes/builtin/base/CommandArgs.java

...tin/src/com/oracle/truffle/r/nodes/builtin/base/Quit.java

...om/oracle/truffle/r/nodes/builtin/fastr/FastRContext.java

...runtime/src/com/oracle/truffle/r/runtime/RCmdOptions.java

....r.runtime/src/com/oracle/truffle/r/runtime/REnvVars.java

....r.runtime/src/com/oracle/truffle/r/runtime/ROptions.java

....r.runtime/src/com/oracle/truffle/r/runtime/RProfile.java

...untime/src/com/oracle/truffle/r/runtime/RStartParams.java

...fle.r.runtime/src/com/oracle/truffle/r/runtime/Utils.java

...src/com/oracle/truffle/r/runtime/context/ContextInfo.java

...me/src/com/oracle/truffle/r/runtime/context/RContext.java