Use the -C dir option which 
Temporarily changes directories (cd dir) during execution of the jar command while processing the following inputfiles argument.
If you execute the jar command in your question and list the contents of temp.jar, you will see output similar to the following:
$ rm -rf temp.jar
$ jar cfe temp.jar SigarTest.SigarMain SigarTest/bin/ tools.jar sigar.jar mongo-2.7.3.jar
$ jar tf temp.jar
META-INF/
META-INF/MANIFEST.MF
SigarTest/bin/
SigarTest/bin/SigarTest/
SigarTest/bin/SigarTest/SigarMain.class
tools.jar
sigar.jar
mongo-2.7.3.jar
$ java -jar temp.jar
Exception in thread "main" java.lang.NoClassDefFoundError: SigarTest/SigarMain
Caused by: java.lang.ClassNotFoundException: SigarTest.SigarMain
    at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Note that having SigarTest/bin in temp.jar is incorrect. Executing temp.jar throws the ClassNotFoundException since SigarMain is in package SigarTest.bin.SigarTest. Now consider the following jar command that uses the -C dir option:
$ rm -rf temp.jar
$ jar cfe temp.jar SigarTest.SigarMain -C SigarTest/bin/ . tools.jar sigar.jar mongo-2.7.3.jar
$ jar tf temp.jar
META-INF/
META-INF/MANIFEST.MF
SigarTest/
SigarTest/SigarMain.class
tools.jar
sigar.jar
mongo-2.7.3.jar
$ java -jar temp.jar
SigarMain is in the correct package and executing temp.jar does not throw a ClassNotFoundException.