Develop Reference

Javac does compiling always have to be from top of package? (Passing path of package to javac ?)

When compiling java code the I have been told the compiler must be run from the top of the package.
That is if I am trying to compile Test.java which is in tools.testing I have to first set the top of the package hierarchy, the folder containing /tools in order for it to work.
The class I am trying to compile uses another class contained in the same package and as such passing the full path of the code to the compiler prevents it from seeing the other class (as it doesn't search current directory and instead searches for the package inside of itself: ./tools/testing when it is already in /tools/testing )
I wanted to know if this was always the case or if there was a way to, for example: provide the path to the top of the package (since passing full path will not work for me) as an argument of the javac command or something similar ?
Thanks !

You should use an Integrated Development Environment (IDE) like IntelliJ, Eclipse or Netbeans. In an IDE you can create a Java project which has a directory acting as the 'source root'.
If you use Maven as your build tool the default location for such a directory is /src/main/java/ (this is the de-facto standard for Java projects at this time).
The IDE will automatically compile your Java files for you and allow you to run them easily during development.
If you want to run the application stand-alone you have to package it in some way. One simple and effective way is to generate a .jar file which contains all the .class files and other files you need (like images, .properties files etc). If you specify a pom.xml file for your project (that's Maven again) and set the packaging to jar Maven will automatically create a .jar file for you. You can even make the .jar file runnable with some additional settings.
See also this answer for some more info about packaging.

Shortcut to launch java/scala without specific classpath

I am new to scala. Now I start to use the testing framework scalatest. But every time I run the test, I need to type scala -cp /path/to/jar/folder/scalatest_2.11-2.2.1.jar my_test.scala to include the scalatest package.
I want to type less. Here is what I think may work.
Put export CLASSPATH=/path/to/jar/folder/scalatest_2.11-2.2.1.jar;$CLASSPATH in .bashrc .
Put alias scalat="scala -cp /path/to/jar/folder/scalatest_2.11-2.2.1.jar" in .bashrc .
But I wanna know what is the common way to let scala/java know package without specific it in CLASSPATH in scala/java community?

The usual way is to use a build system like SBT or Maven (with the scala plugin) to manage your dependencies, classpath and build cycle.

Are Tomcat jars meant to be added to the classpath?

Since jars like servlet.jar are usually not downloaded on their own, but rather come part of tomcat/lib folder, should I just add an entry to them in the classpath? Is that the common practice?
I use Ubuntu.

You only need to reference them yourself when you want to compile servlet classes. How to do that depends in turn on the tools used for compilation.
If you're using plain javac, then you could reference them in %CLASSPATH%. But even then, that's considered a poor practice since that would potentially pollute the default classpath of all other Java compilations/applications. Rather write a shell file which sets the classpath right on the current execution environment by utilizing the -cp attribute of javac command.
If you're using a bit decent IDE like Eclipse/Netbeans, then you should just integrate the server in the IDE and associate the project with it. The IDE will then take care about setting the buildpath right. You don't need to set any environment variables then.
You do not need to reference them when you want to run them. The servletcontainer will take care about it by itself.
See also:
How do I import Servlet API in Eclipse?

If you are running a web application on Tomcat then the servlet-api.jar is in the classpath.

best way to deploy a package

When I finished to write my classes I put them into a package structure and then I jarred all.
Now which is the best way to deploy and use my jar?
setting classpath;
use CLASSPATH variable;
using the extension mechanism.

Don't update the user's CLASSPATH environment variable because there is a risk that your deployed application will interfere with other Java applications that the user might want to run.
Don't deploy using the Extension mechanism because there is a risk that you will interfere with applications run by any user using the JVM that you have "extended".
The best solution is to create and deploy a wrapper script that uses the "-cp" argument, or a shortcut that runs a self-launching JAR file ... as suggested by other answers.

I you have a main class in that jar that you want to run the best approach is to put a META-INF/MANIFEST.MF file in the jar and launch your class using java -jar mypackage.jar
The manifest should contain a Class-Path and a Main-Class attribute
See http://java.sun.com/j2se/1.3/docs/guide/jar/jar.html#JAR%20Manifest

If you mean by 'deploy and use' that you want to use it in another application, set it on the classpath of that application.
If you use the extension mechanism (I assume you mean putting the jar in pathtojava/lib/ext) every application using that jvm will have the jar loaded, the samecounts for the CLASSPATH as system variable. That is most likely not necessary?
If you ment to execute/use the jar as standalone application; just run it commandline, no classpath stuff needed. If you want to deploy on a server you probably wanted to make a war or ear fiel instead.

Best to my opinon is to provide batch files and shell scripts to start the application.
Sophisticated scripts check for environment variables like $JAVA_HOME (%JAVA_HOME%) and use them, if defined or use a default value.
Inside the script you could build the classpath in an internal variable and start the app with a line like
%JAVA_HOME%\bin\java.exe -cp %LIBRARIES% com.example.Main
I would prefer this solution over the java -jar Application.jar alternative, because this one requires that you setup the classpath inside the jars manifest. So deploying an application that depends on existing libraries on the target system is pretty difficults, just because you have to know the library paths before you build the application.

Setting the classpath (using -cp) is the best way, as you can have a different classpath for each application. The CLASSPATH environment variable is global for all Java applications running on the machine, as is the extension mechanism so you probably don't want to use those.
If your code is executable (ie it has a public static void main(String[] args) method) then you can also specify the class that the main method is in, and the associated classpath within the manifest file inside the Jar file. Once you have done that you can do this:
java -jar myJar.jar
And Java will work out the rest.

How do I include java stuff in .jar files?

Okay. So here's my question: I am making a data parser in Clojure. One part of my program is that it has to be able to graph the data. I figure, I'll use jFreeChart. However, I have absolutely NO IDEA how to include stuff in JAR files. What I mean is: if I have a app.jar file in my classpath, I don't seem to be able to do:
import app.thing.thing2
without changing the classpath to be inside the jar file.
The idea here is that I don't think I can change my classpath since I need to set it to run Clojure (Or do I?). The global classpath is currently /usr/share/java.
And please don't ask me to use Maven, Ant or any project-building tool unless it is the only way to do this. This is a script for personal use that doesn't need or want a whole lot of overhead.
I wonder if I should just unpack every JAR file, so that I can reference the directory structure? Is this bad?
Let me know if you need any clarifications!

The content of the (Java) CLASSPATH environment variable is available to Clojure so if you add your jar to the global classpath before to run Clojure, you'll "see" it:
export CLASSPATH=/path/to/jfreechart.jar:$CLASSPATH
But, in my opinion, this is not the "clean" way to add a jar to Clojure's classpath (because this makes the library visible to any Java program and may not be desired). Instead, you should use the CLOJURE_EXT environment variable. This is how this variable is documented:
# CLOJURE_EXT The path to a directory containing (either directly or as
# symbolic links) jar files and/or directories whose paths
# should be in Clojure's classpath. The value of the
# CLASSPATH environment variable for Clojure will be a list
# of these paths followed by the previous value of CLASSPATH
# (if any).
On my system, it is defined as below:
export CLOJURE_EXT=~/.clojure
So, to add jfreechart.jar (or any other library) to Clojures's classpath, copy it (or add a symlink pointing to it) in the directory defined in the CLOJURE_EXT variable.
And by the way (I'm sorry but your question is not that clear), if you want to bundle some Java classes into a jar, the command is something like that:
$ jar cf myjarfile *.class
You'll find documentation of jar - the Java Archive Tool - here.

I completely respect your desire not to use a project management tool, though I just spent longer typing this sentence than it takes to set up leiningen. For your one-off script any tool is going to be overkill and Pascal Thivent's answer covers this very well. For people reading this question who perhaps want to produce a jar file, or easily load their Clojure into emacs/slime-swank I cant recommend leiningen too strongly.

If you going to basics you can inline your classpath to include the hardcoded location of your jars, so if you on windows it will look something like
java -cp .;%CLASSPATH%;C:/here/it/is/foo.jar com.foo.MyClass

Not sure how clojure is run, but don't you just add the jar file to the classpath?
i.e.
/usr/share/java:/home/user/myjarfile.jar