I found that this problem has been introduced from following commit for JENKINS-15120.

f7330d7a158eff6705706b1f812993a9b918c351 is the first bad commit
commit f7330d7a158eff6705706b1f812993a9b918c351
Author: Kohsuke Kawaguchi <[email protected]>
Date:   Sat Jun 8 12:21:18 2013 +0300

    [FIXED JENKINS-15120]
    
    - integrated the newer release of remoting
    - jar caching won't work with class file directory, so plugin
      WEB-INF/classes are now exploded as WEB-INF/lib/classes.jar
      (This should also solve the problem of slow plugin extraction in the
      presene of Anti-virus software on Windows.)
    - because the structure of the exploded jar file has changed, I changed
      the up-to-date check timestamp file name to force re-extraction in
      existing installations.

:100644 100644 b62d2499495def2906db363fb3abc6283f1ad445 062b8e4bde3a169d0e6439c4d20e93365a51ff98 M      changelog.html
:040000 040000 7623c02dcc413e8e2c8c8cf961eb766163e77e3b 9d5c2e08651149192680e123de36d7616a3087e7 M      core
:040000 040000 ac627254e2446ddb45752fad05955a5dd63578fc b54c1ea17ca49034cc5eaf700f085cc6f237764e M      maven-plugin
:100644 100644 39b28080756b0b707c5f09b4c97ba97b9fb86aaa b071d7747ef3eb25ead1551c6377a3400de64e6a M      pom.xml
bisect run success
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