javac : command not found

You installed the Java Runtime Environment (JRE) only, which does not contain javac. For javac, you have to install the OpenJDK Development Environment. You can install java-devel or java-1.6.0-openjdk-devel, which both include javac.

By the way: you can find out which package provides javac with a yum search, e.g.

su -c 'yum provides javac'

on more recent releases of CentOS e.g. 6 the command changes to

su -c 'yum provides */javac'

Another note: using yum and openjdk is only one possibility to install the JDK. Many people prefer Sun/Oracle's "original" SDK. See How to install Java SDK on CentOS? and links for alternatives.

You shouldn't set your classpath to point to your JDK bin directory -- instead it should be the PATH environment variable, which serves a different purpose to classpath. (The classpath defines a list of jars and directories containing compiled Java .class code; the PATH variable defines a list of paths where the shell needs to look and locate programs to execute when they are not found in the current directory -- so if you type for instance zip -- it would look in all the directories defined in PATH and figure out that zip program is located under /usr/bin) Secondly if you want to compile sources from both directory you need to specify:

• all the paths where the sources are (both home/pathToFolderA/src and home/pathToFolderB/gen-java)
• the path where the compiled .class files to be generated
• specify in the classpath any library you might use in your source files

To sum it up, it would be something like this to compile:

javac -d /home/pathToFolderWithResultsOfCompilation -classpath /path/to/some.jar:/path/to/another.jar home/pathToFolderA/src/*.java home/pathToFolderB/gen-java/*.java 

and to run your compiled programs:

java -classpath /path/to/some.jar:/path/to/another.jar:/home/pathToFolderWithResultsOfCompilation full.name.of.your.Java

Run alternatives --config java to pick the Java version you want to use as default. It will print out a list of installed Javas to choose from.

which java, however, will always print out /usr/bin/java. This doesn't mean it's set wrong! Observe:

$ ls -l `which java`
lrwxrwxrwx 1 root root 22 Oct 19 11:49 /usr/bin/java -> /etc/alternatives/java
$ ls -l /etc/alternatives/java
lrwxrwxrwx 1 root root 35 Oct 19 11:49 /etc/alternatives/java -> /usr/lib/jvm/jre-1.5.0-gcj/bin/java

If you use alternatives to change the path to IcedTea, ls -l /etc/alternatives/java will reflect that.