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Is Java required to run some .NET based programs?

Introduction

One of the comments to this question is about using GnuWin's file command in order to check whether a program is using java or not. However GnuWin's file command indicates the following:

C:\Windows\system32>file "C:\Program Files\Eclipse Foundation\eclipse\eclipse.exe"
C:\Program Files\Eclipse Foundation\eclipse\eclipse.exe; PE32+ executable for MS
 Windows (GUI) Mono/.Net assembly

C:\Windows\system32>

while java is required in order to run programs, eg Eclipse, ApacheDS, Apache Directory Studio and Tomcat.

The discussion regarding this question resulted in a suggestion to ask a question at StackOverflow regarding the relation between .NET based programs and Java processes.

Question

Why does GnuWin's File Command indicate that certain programs are .Net based, while these require Java in order to run?

Eclipse.exe is not a java program: it is actually a native win32 executable that serves simply to locate and launch the JVM with appropriate commandline parameters and the path to the JAR file that contains the actual Eclipse java executable.

See for example http://help.eclipse.org/juno/index.jsp?topic=%2Forg.eclipse.platform.doc.isv%2Freference%2Fmisc%2Flauncher.html for full details.

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