com.sun.tools.javadoc.Main is reading .java files before genExceptions.sh has finished writing them:

genExceptions.sh:

SCRIPTS="/cygdrive/c/jprt/T/P1/205021.tbell/s/jdk/make/scripts" NAWK="/cygdrive/c/cygwin/bin/gawk" SH="/cygdrive/c/cygwin/bin/sh" /cygdrive/c/cygwin/bin/sh /cygdrive/c/jprt/T/P1/205021.tbell/s/jdk/make/scripts/genExceptions.sh /cygdrive/c/jprt/T/P1/205021.tbell/s/jdk/src/share/classes/java/nio/channels/exceptions /cygdrive/c/jprt/T/P1/205021.tbell/s/build/windows-x86_64-normal-server-fastdebug/jdk/gensrc/java/nio/channels
/cygdrive/c/cygwin/bin/mkdir -p /cygdrive/c/jprt/T/P1/205021.tbell/s/build/windows-x86_64-normal-server-fastdebug/jdk/gensrc_no_srczip/javax/swing
--> /cygdrive/c/jprt/T/P1/205021.tbell/s/build/windows-x86_64-normal-server-fastdebug/jdk/gensrc/java/nio/channels/ClosedChannelException.java
--> /cygdrive/c/jprt/T/P1/205021.tbell/s/build/windows-x86_64-normal-server-fastdebug/jdk/gensrc/java/nio/channels/FileLockInterruptionException.java
--> /cygdrive/c/jprt/T/P1/205021.tbell/s/build/windows-x86_64-normal-server-fastdebug/jdk/gensrc/java/nio/channels/AsynchronousCloseException.java

[...]

javadoc:

Constructing Javadoc information...
c:\jprt\T\P1\205021.tbell\s\build\windows-x86_64-normal-server-fastdebug\jdk\gensrc\java\nio\channels\AsynchronousCloseException.java:1: error: unclosed comment
/*
^
c:\jprt\T\P1\205021.tbell\s\build\windows-x86_64-normal-server-fastdebug\jdk\gensrc\java\nio\channels\AsynchronousCloseException.java:3: error: reached end of file while parsing
c:\jprt\T\P1\205021.tbell\s\jdk\src\share\classes\java\nio\channels\spi\AbstractInterruptibleChannel.java:196: error: cannot access AsynchronousCloseException
        throws AsynchronousCloseException
               ^
  bad source file: c:\jprt\T\P1\205021.tbell\s\build\windows-x86_64-normal-server-fastdebug\jdk\gensrc\java\nio\channels\AsynchronousCloseException.java
    file does not contain class java.nio.channels.AsynchronousCloseException
    Please remove or make sure it appears in the correct subdirectory of the sourcepath.
3 errors



See attached log file: windows_x64_6.2-fastdebug.log.FAILED.log