After some investigation,
the initial clone causes the corrupt.

On the initial cloning,

hudson.plugins.git.GitSCM#fetchSubmodulesFrom

is called. And then,

hudson.plugins.git.IGitAPI#fetch (by subGit.fetch(submoduleRemoteRepository);)

is called.


After that, the result of tree command, which is for WORKSPACE/test0/.git, is:

.git
├── FETCH_HEAD
├── HEAD
├── branches
├── config
├── description
├── hooks
│   ├── applypatch-msg.sample
│   ├── commit-msg.sample
│   ├── post-update.sample
│   ├── pre-applypatch.sample
│   ├── pre-commit.sample
│   ├── pre-rebase.sample
│   ├── prepare-commit-msg.sample
│   └── update.sample
├── index
├── info
│   └── exclude
├── logs
│   ├── HEAD
│   └── refs
│       ├── heads
│       │   └── master
│       └── remotes
│           └── origin
│               ├── b_tagOfModule1
│               └── master
├── objects
│   ├── 27
│   │   └── 31d33c38b55dc717a0d644571eea30ec3a00e3
│   ├── 61
│   │   └── 064ef71976703c49eb13ece2030c89965b7145
│   ├── 66
│   │   └── 52ffc1ee608a2bf7be49b8ead0526182b1d52b
│   ├── 82
│   │   └── 818b9b6f0420237a8c1a5e6e771e900b7a79d2
│   ├── 9d
│   │   └── 7a672db165435d85eb807192b218cdcaed340f
│   ├── a8
│   │   └── edc5644debf0e6600164c8fe13f83e785a9b1a
│   ├── ca
│   │   └── f1aee9a48387b6d9cbeab47958ed2def5a3bd1
│   ├── e6
│   │   ├── 46e34bbd8d13586015757ad5e227617c9513e8
│   │   └── 9de29bb2d1d6434b8b29ae775ad8c2e48c5391
│   ├── f8
│   │   └── 53768ca5aa9df82f889cda025f166bf59abdb4
│   ├── info
│   └── pack
├── packed-refs
└── refs
    ├── heads
    │   └── master
    ├── remotes
    │   └── origin
    │       ├── HEAD
    │       ├── b_tagOfModule1
    │       └── master
    └── tags
        └── tagOfModule1

b_tagOfModule1 the above is may strange, because that is of submodule (module1) tag, not root's.

A repository structure is created by the testcase I mentioned before: https://github.com/comutt/git-plugin/commit/09d16e20592e206f2de64017bb2276124ba2d443

And I apologize that I have no more time to investigate,
and may not fix this problem.

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