For medium and big size software projects its very difficult to manage everything with just educational way. As a example Open Office created with JAVA but if they will taken approach as write JAVA class in native OS editor after that compile and run from command/Shell prompt then it will be very painful for developer.
So for software project we need to move with systematic way. As use of some good IDE(Integrated Development Environment). Below is the approach how we can move,
PHP Environment
Apache, MySQL, PHP, Composer, NotePad++
JAVA Environment
Eclipse/Netbeans, Ant, JDK and JRE
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Create Development Environment for Software Based Projects,