Sometimes workspace fails to start or projects are failed to initialize

[mmorhun]

Sometimes when try to start workspace from Java-MySQL stack, it fails to start with error in dev-machine logs:

che.log.txt

Sometimes it starts, but projects initialization fails, as a consequence Explorer panel doesn't appear and nothing happens on click on it.

Reproduction Steps:

1. Go to dashboard, create a workspace from Java MySQL stack with petclinic project from samples.
2. Wait until workspace starts.
3. Stop it and return to dashboard -> workspaces
4. In the list of workspaces click run on the just created workspace, then go to details of the workspace and click open button. Wait until the workspace starts. See start logs in IDE.
5. If workspace starts successfully, stop it and repeat step 4. If workspace starts, but projects fail to initialize - second scenario happens. To reproduce first one go to 1st step.

Expected behavior:
Workspace should start correctly.

Observed behavior:
Workspace fail to start with timeout error. See real reasons in start logs.
Also possible that workspace can start, but projects fail to initialize.

Che version:
OS and version: Ubuntu 16.04 LTS
Docker version: Version: 1.12.3, API: 1.24
Che install: server (zip)

Additional information:

• Problem started happening recently, didn't happen in an older version of Che: Yes
• Problem can be reliably reproduced, doesn't happen randomly: No, ~ 1 of 3 cases.
  

[mmorhun]

Just reproduced both cases on nightly:
Version :5.0.0-M9-SNAPSHOT
Revision :2bf4f8cecbb729f2
Build Time :2016-12-12 19:18:04
nightly.log.txt

[mmorhun]

Reproduced it on Java stack with Spring sample project on nightly