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[news.eclipse.tools] M4 flexible project structure

I am trying to use the new flexible project structures in M4 and find that I
cannot even get off the ground. A greatly simplified version of our source
tree is shown below:

Base
   Release5 -- This should be the root of an Eclipse workspace
      doc
      classes --- The output tree
      src
          cpp
          java
          java-infrastructure
          java-test
   Release6 -- This should be the root of an Eclipse workspace
     doc
    classes --- The output tree
     src
         cpp
         java  ---- The root for all files that make up the shippable code
              com ---- The root of the package structure
                     cryptocard
                         cryptoadmin
                         utilities  --- Source files live here
                             configuration ---- Source files live here
                             gui --- Source files live here
                             ui --- Source files live here
         java-infrastructure --- Stuff that supports the development effort
but is not shippable
         java-test -- The root for all test files - a parallel package
structure to the java tree is maintained
              com ---- The root of the package structure
                     cryptocard
                         cryptoadmin
                         utilities  --- Source files live here
                             configuration ---- Source files live here
                             gui --- Source files live here
                             ui --- Source files live here

The ground rules include the restriction that new directory levels may NOT
be inserted into the tree, however new sub-trees can be added. Also,
changing the single rooted structure of the source tree is not an option.

I started with the problem of creating a project that would handle the
contents of the "utilities" directory without handling any of the
sub-directories. The first issue was to find a location to place the project
files. I created a directory under "base/release 6" called "projects" and
tried to create a new java project called com.cryptocard.utilities-6.0 in
this directory. However the new project wizard disallowed this with the
following diagnostic:

   "Project contents cannot be inside workspace directory"

I have two questions.
1. What rule did I break to cause the diagnostic?
2. Assuming that the first problem can be solved, is there enough
functionality in the new flexible project structure support to allow me to
create a project that manages the "utilities" directory, and separate
projects that manage the "configuration", "gui", and "ui" directories that
exist under the "utilities" directory.
If I can do this, I can handle our entire source tree without difficulties.

Regards

Jonathan Gossage