I believe this is fixed on master.  I have updated the demo site with the latest snapshot
and created symlinks to existing repositories.  You are welcome to build from source
to determine if I have fixed your issue.

Indeed, repository listing now works in master however there's an exception pushing
changes to a symlinked repo. Works for non-symlinked:
java.lang.NullPointerException
        at org.eclipse.jgit.transport.resolver.FileResolver.isUnreasonableName(FileResolver.java:237)
        at org.eclipse.jgit.transport.resolver.FileResolver.open(FileResolver.java:96)
        at com.gitblit.GitBlit.getRepository(GitBlit.java:771)
        at com.gitblit.GitBlit.getRepository(GitBlit.java:758)
        at com.gitblit.GitBlit.getRepositoryModel(GitBlit.java:863)
        at com.gitblit.GitServlet$GitblitReceiveHook.getRepositoryModel(GitServlet.java:218)
        at com.gitblit.GitServlet$GitblitReceiveHook.onPreReceive(GitServlet.java:170)
        at org.eclipse.jgit.transport.ReceivePack.service(ReceivePack.java:179)
        at org.eclipse.jgit.transport.ReceivePack.receive(ReceivePack.java:142)
        at org.eclipse.jgit.http.server.ReceivePackServlet.doPost(ReceivePackServlet.java:174)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:688)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:770)
        at org.eclipse.jgit.http.server.glue.UrlPipeline$Chain.doFilter(UrlPipeline.java:237)
        at org.eclipse.jgit.http.server.ReceivePackServlet$Factory.doFilter(ReceivePackServlet.java:139)
        at org.eclipse.jgit.http.server.glue.UrlPipeline$Chain.doFilter(UrlPipeline.java:235)
        at org.eclipse.jgit.http.server.RepositoryFilter.doFilter(RepositoryFilter.java:151)
        at org.eclipse.jgit.http.server.glue.UrlPipeline$Chain.doFilter(UrlPipeline.java:235)
        at org.eclipse.jgit.http.server.NoCacheFilter.doFilter(NoCacheFilter.java:80)
        at org.eclipse.jgit.http.server.glue.UrlPipeline$Chain.doFilter(UrlPipeline.java:235)
        at org.eclipse.jgit.http.server.glue.UrlPipeline.service(UrlPipeline.java:215)
        at org.eclipse.jgit.http.server.glue.SuffixPipeline.service(SuffixPipeline.java:101)
        at org.eclipse.jgit.http.server.glue.MetaFilter.doFilter(MetaFilter.java:163)
        at org.eclipse.jgit.http.server.glue.MetaServlet.service(MetaServlet.java:133)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:770)
        at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:538)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1352)
        at org.apache.wicket.protocol.http.WicketFilter.doFilter(WicketFilter.java:294)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
        at com.gitblit.AccessRestrictionFilter.doFilter(AccessRestrictionFilter.java:184)
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1323)
    ...

I'll setup a test to debug pushing.  In the meantime, perhaps you could inject something
like the following @ line 217 of com.gitblit.GitServlet:

try {
  System.out.println(GitBlit.getRepositoriesFolder());
  System.out.println(GitBlit.getRepositoriesFolder().getCanonicalPath());
  System.out.println(repository.getDirectory());
} catch (IOException e) {
  e.printStackTrace();
}

And then push.  The code is attempting to find the model class for the repository from
it's filesystem path.  This is the reverse of what we usually do, map a model class
to a directory.

Tried it and the output for these calls appears correct:
  GitBlit.getRepositoriesFolder(): /srv/git
  GitBlit.getRepositoriesFolder().getCanonicalPath(): /srv/git
  repository.getDirectory(): /home/gitdaemon/test

But 'repositoryName' becomes null on this line and that seems to cause the problem:
  String repositoryName = FileUtils.getRelativePath(...)

Notes: '/srv/git' is my git repository folder. It has a symlink called 'test' that
points to '/home/gitdaemon/test'

Yup.  I just thought of that kinda of layout while I was out for a few minutes.  My
current push design is a complete failure for symlinks.  My code tries to find a relationship
between those two paths and there is none for already resolved symlinks.

This will require a different design to get the repository model or perhaps I can cache
the model earlier during the request.  This wasn't a great design anyways - but it
worked within the constraints of JGit.

I'll let you know when I have code for you to test.

I tried a small workaround and it seems to solve the issue. In GitblitReceiveHook:
        protected RepositoryModel getRepositoryModel(ReceivePack rp) {
            Repository repository = rp.getRepository();
            return GitBlit.self().getRepositoryModel(repository.getDirectory().getName(), repository);
        }

I added the GitBlit.getRepositoryModel method that takes a repository and does not
look it up.

Ah that would work too.  I just pushed a change which I'd like you to try out.

I like your change because it is smaller, but we lose the repository name which is Gitblit's
id for the repo.  This can affect the push hooks which is the main reason we need to
grab the "real" model.  My change determines the repo name from the request and caches
it for re-use in the hooks.  This means that data and downstream behavior is identical
to current release.

Yepp, push works with the latest fix. We're not using any hooks though so I can't tell
if those are working.
Thanks.

Hook unit tests pass, so I am confident they are working.

Fix/change released in 1.1.0.