Embedding Gradle via tooling API is somewhat inconvenient. The number of jars seems to be slowly growing and since Gradle 1.1 it also incudes jars that might clash with client jars:

jsr305-1.3.9.jar
guava-11.0.2.jar

• Ideally, the tooling-api ships in a single jar that only contains what's really needed.
• We should consider repackaging the 3rd party libs to avoid conflicts

This inconvenience might lead to incorrect use of the Tooling API. Like in JetGradle, the jars are autodiscovered from the user provided gradle installation which leads to various awkward problems (the tooling api jars and its dependencies must be included in the client distribution, not autodiscovered).