why same class file in eclipse not overwriting and showing error type already defined

EDIT: Okay, through comments I think we've actually got to the bottom of the problem. The situation is:

• Compiling under Windows
• There are two classes in the same file, with the same name except for case
• The command-line compiler doesn't noticed that the two class files will become one due to Windows file system case-insensitivity, but Eclipse does

So as an example:

class Foo {}
class foo {}

The Eclipse error message also makes this pretty clear, by mentioning case:

Class file collision: A resource exists with a different case: '/Sandbox/bin/Foo.class'.

As with my earlier answer, my advice is still the same don't do this.

---

Earlier answer...

I suspect that when you used the same name in a different file and compiled from the command line, you only specified one of them to compile - whereas Eclipse will try to compile all the classes present. If you specified both of the files, you would have got an error:

For example:

X.java
class Foo {}

Y.java
class Foo {}

> javac X.java Y.java
Y.java:1: error: duplicate class: Foo
class Foo {}
^
1 error

Basically, don't do this. Either rename one of the classes, or delete one of the files.