[news.eclipse.newcomer] Java project: linked source vs NTFS junction

["Ryan Fong" <rfong@xxxxxxxxxxxxxxxxxxx>]

I currently have our eclipse projects set up using linked resources & linked 
classpaths so that the project links files relatively.  It's like this:

c:\
project
    workspace
        project1    SOURCE=c:\project\src, TOOLS=c:\project\tools
    src                // .java files
    tools             // 3rd party jars

However, this is a pain to define on every branch, so I am using NTFS 
junctions/Linux links to create this:
c:\
project
    workspace
        project1
            src     -> ../../src
            tools  -> ../../tools
    src
    tools

However, once I do this, everything in Eclipse is incredibly slow!!!  The 
source linkage before/after is the same since src has further 
subdirectories, so there isn't ever a full inclusion of src anywhere.  The 
tools linkage appears to cause the majority of the slowdown.  Is there a 
guideline for project structuring that can also explain this slow response?