The things you mention are no fun either (`node-gyp` in particular), but the Java issues I encountered were far beyond run-of-the-mill runtime linking and interop issues you describe. The details are lost to time and a bit fuzzy but I recall the primary issue being competing CDI implementations stepping on each other when we tried to use JSF with a recent version of Spring... and because most everything in the Java ecosystem was doing some opaque Aspect4J magic it was nigh-impossible to debug.