A DESCRIPTION OF THE PROBLEM :
JNI headers generator maps classnames to headers names by replasing all dots (.) to underscores (_) in full classname.

Compiler doesn't handle case when several classes mapped into same header.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
File example.java:
package com;
class example { native void x(); }

File com_example.java
// no package
class com_example { native void y(); }

run: javac -h include example.java com_example.java

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
File com_example.h:

JNIEXPORT void JNICALL Java_com_example_x(JNIEnv *, jobject);
JNIEXPORT void JNICALL Java_com_1example_y(JNIEnv *, jobject);
ACTUAL -
File com_example.h:

// functions only from last file in list
JNIEXPORT void JNICALL Java_com_1example_y(JNIEnv *, jobject);

FREQUENCY : always