JarIndexer mishandles paths with the extension in multiple elements

FileNotFoundException for some JAR file paths when the index file path is constructed.

The problem appears to be in org.jboss.jandex.JarIndexer#getIndexFile(File, boolean), wherein every occurrence of the extension is replaced in the entire JAR file path, such that path elements that include the extension (e.g., ".jar") are incorrectly modified.
An example from Jandex used in an Arquillian context:
/private/var/folders/41/qy6ftgc53mn4v01s3xnytzgc0000gq/T/arquillian8152228539718351683MyTestApp.jar/MyTestApp.jar
where arquillian8152228539718351683MyTestApp.jar is a directory, and the resulting index file path is
/private/var/folders/41/qy6ftgc53mn4v01s3xnytzgc0000gq/T/arquillian8152228539718351683MyTestApp-jar/MyTestApp-jar.idx
and there is no valid directory named arquillian8152228539718351683MyTestApp-jar