#one file
perl -i -0pe 's|//.*?\n|\n|g; s#/\*(.|\n)*?\*/##g;' file.java

#multiple files
find . -name "*.java" -type f | while read fname; do   perl -i -0pe 's|//.*?\n|\n|g; s#/\*(.|\n)*?\*/##g;' "$fname"; done