java側linuxのzipコマンドを呼び出したい場合、ProcessBuilderを利用できます。
例１：
全部ディレクトリ保持の場合、
List commandList = new ArrayList();
commandList.add("-r");
ProcessBuilder pb =new ProcessBuilder(commandList);

例２：
ディレクトリ保持しない場合、（同じファイル名あれば、エラー）
List commandList = new ArrayList();
commandList.add("-j");
ProcessBuilder pb =new ProcessBuilder(commandList);
LINUXのzipコマンド一覧
-f freshen: only changed files
-u update: only changed or new files
-d delete entries in zipfile
-m move into zipfile (delete OS files)
-r recurse into directories
-j junk (don't record) directory names
-0 store only
-l convert LF to CR LF (-ll CR LF to LF)
-1 compress faster
-9 compress better
-q quiet operation
-v verbose operation/print version info
-c add one-line comments
-z add zipfile comment
-@ read names from stdin
-o make zipfile as old as latest entry
-x exclude the following names
-i include only the following names
-F fix zipfile (-FF try harder)
-D do not add directory entries
-A adjust self-extracting exe
-J junk zipfile prefix (unzipsfx)
-T test zipfile integrity
-X eXclude eXtra file attributes
-y store symbolic links as the link instead of the referenced file
-e encrypt
-n don't compress these suffixes

例３下記の場合はどうする？
フォルダの形式：/home/AB/CD/+各種ファイルとサブフォルダ
入力パース
/home/AB/CD/
圧縮後（/home/AB/CD/含まない）
各種ファイルとサブフォルダ.zip
試して、下記のコマンドはいいです。

pb = new ProcessBuilder("sh", "-c", “zip -r test.zip ./*”)).directory(new File("/home/AB/CD/"));
同じく書きの書き方でもいいです。
pb = new ProcessBuilder("/bin/sh", "-c", “zip -r test.zip ./*”)).directory(new File("/home/AB/CD/"));
pb = new ProcessBuilder("/bin/bash", "-c", “zip -r test.zip ./*”)).directory(new File("/home/AB/CD/"));