Hello,
Since I upgraded to EGit 
2.0 (rc2 and now rc3) I am unable to fetch from Git repositories over 
SSH. I am getting the exception enclosed below.
As a note, the 
server's key *is* in know_hosts file. The variable HOME is correctly set
 up. The strange part is that this server uses password authentication 
for SSH access, not private key.
Let me know if you need further information.
Thanks,
Alex
org.eclipse.core.runtime.CoreException: ssh://alex@server/opt/git/Cache.git: Cannot find SSH keys.
    at org.eclipse.egit.ui.internal.fetch.FetchOperationUI.execute(FetchOperationUI.java:102)
    at org.eclipse.egit.ui.internal.fetch.FetchOperationUI$1.run(FetchOperationUI.java:117)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:54)
Caused by: org.eclipse.jgit.api.errors.TransportException: ssh://alex@server/opt/git/Cache.git: Cannot find SSH keys.
    at org.eclipse.jgit.api.FetchCommand.call(FetchCommand.java:137)
    at org.eclipse.egit.core.op.FetchOperation.run(FetchOperation.java:127)
    at org.eclipse.egit.ui.internal.fetch.FetchOperationUI.execute(FetchOperationUI.java:99)
    ... 2 more
Caused by: org.eclipse.jgit.errors.TransportException: ssh://alex@server/opt/git/Cache.git: Cannot find SSH keys.
    at org.eclipse.jgit.transport.JschConfigSessionFactory.getSession(JschConfigSessionFactory.java:142)
    at org.eclipse.jgit.transport.SshTransport.getSession(SshTransport.java:121)
    at org.eclipse.jgit.transport.TransportGitSsh$SshFetchConnection.<init>(TransportGitSsh.java:248)
    at org.eclipse.jgit.transport.TransportGitSsh.openFetch(TransportGitSsh.java:147)
    at org.eclipse.jgit.transport.FetchProcess.executeImp(FetchProcess.java:127)
    at org.eclipse.jgit.transport.FetchProcess.execute(FetchProcess.java:113)
    at org.eclipse.jgit.transport.Transport.fetch(Transport.java:1069)
    at org.eclipse.jgit.api.FetchCommand.call(FetchCommand.java:128)
    ... 4 more
Caused by: com.jcraft.jsch.JSchException: Cannot find SSH keys.
    at org.eclipse.egit.ui.EclipseSshSessionFactory.createSession(EclipseSshSessionFactory.java:47)
    at org.eclipse.jgit.transport.JschConfigSessionFactory.createSession(JschConfigSessionFactory.java:150)
    at org.eclipse.jgit.transport.JschConfigSessionFactory.getSession(JschConfigSessionFactory.java:109)
    ... 11 more
eclipse.buildId=I20120524-2100
java.version=1.6.0_29
java.vendor=Sun Microsystems Inc.
BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=en_US
Framework arguments:  -product org.eclipse.epp.package.jee.product
Command-line arguments:  -os win32 -ws win32 -arch x86_64 -product org.eclipse.epp.package.jee.product