Use of cygwin can create some very unpredictable build issues, the cygwin BLODA (Big List of Dodgy Apps) at http://cygwin.com/faq/faq.using.html#faq.using.bloda should be documented.
Some of these apps can cause rm and unzip failures during the build.

This should be documented in the build readme.

Some examples:

...
jar -xfv ArcTest.jar \
     -J-XX:-PrintVMOptions -J-XX:+UnlockDiagnosticVMOptions \
     -J-XX:-LogVMOutput -J-client -J-Xmx640m -J-Xms128m -J-XX:PermSize=32m -J-XX:MaxPermSize=160m && \
rm -f -r META-INF ArcTest.jar && \
if [ -w hotspot.log ] ; then rm -f hotspot.log; fi )
 created: META-INF/
inflated: META-INF/MANIFEST.MF
inflated: ArcCanvas.class
inflated: ArcControls.class
inflated: ArcTest.class
inflated: example1.html
inflated: IntegerTextField.class
rm: cannot remove directory `META-INF': Directory not empty
make[6]: *** [bundles] Error 1
make[6]: Leaving directory
/cygdrive/c/OpenJDK/jdk7/jdk/make/mkdemo/applets/ArcTest'

---

...
( cd C:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/BarChart && /usr/bin/unzip -o src.zip && rm -f src.zip )
Archive: src.zip
  inflating: BarChart.java
  inflating: example1.html
error: cannot create example2.html
        Permission denied
make[6]: *** [bundles] Error 50
make[6]: Leaving directory `/cygdrive/c/OpenJDK/jdk7/jdk/make/mkdemo/applets/BarChartf

---

...
make[7]: Leaving directory `/cygdrive/c/OpenJDK/jdk7/jdk/make/mkdemo/applets/ArcTest'
Expanding jar file into demos area at C:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/ArcTest
( cd C:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/ArcTest && \
  C:/Progra~1/Java/jdk1.6.0_15/bin/jar -xfv ArcTest.jar \
     -J-XX:-PrintVMOptions -J-XX:+UnlockDiagnosticVMOptions -J-XX:-LogVMOutput \
     -J-client -J-Xmx640m -J-Xms128m -J-XX:PermSize=32m -J-XX:MaxPermSize=160m && \
  rm -f -r META-INF ArcTest.jar && \
  if [ -w hotspot.log ] ; then rm -f hotspot.log; fi )
  created: META-INF/
 inflated: META-INF/MANIFEST.MF
 inflated: ArcCanvas.class
 inflated: ArcControls.class
 inflated: ArcTest.class
 inflated: example1.html
 inflated: IntegerTextField.class
rm: cannot remove directory `META-INF': Directory not empty
make[6]: *** [bundles] Error 1
make[6]: Leaving directory `/cygdrive/c/OpenJDK/jdk7/jdk/make/mkdemo/applets/ArcTest'

---

( cd c:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/BarChart && /usr/bin/unzip -o src.zip && rm -f src.zip )
Archive: src.zip
  inflating: BarChart.java
  inflating: example1.html
error: cannot create example2.html
make[6]: *** [bundles] Error 50
make[6]: Leaving directory `/cygdrive/c/OpenJDK/jdk7/jdk/make/mkdemo/applets/BarChart'

---

...
( cd c:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/ArcTest && \
  C:/Progra~1/Java/jdk1.6.0_15/bin/jar -xfv ArcTest.jar \
     -J-XX:-PrintVMOptions -J-XX:+UnlockDiagnosticVMOptions -J-XX:-LogVMOutput \
     -J-client -J-Xmx640m -J-Xms128m -J-XX:PermSize=32m -J-XX:MaxPermSize=160m && \
  rm -f -r META-INF ArcTest.jar && \
  if [ -w hotspot.log ] ; then rm -f hotspot.log; fi )
  created: META-INF/
 inflated: META-INF/MANIFEST.MF
 inflated: ArcCanvas.class
 inflated: ArcControls.class
 inflated: ArcTest.class
 inflated: example1.html
 inflated: IntegerTextField.class
Expanding source into demos area at c:/OpenJDK/jdk7/build/windows-i586-fastdebug
/demo/applets/ArcTest
( cd c:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/ArcTest && /usr/bin/unzip -o src.zip && rm -f src.zip )
Archive: src.zip
  inflating: ArcTest.java
error: cannot create example1.html
make[6]: *** [bundles] Error 50
make[6]: Leaving directory `/cygdrive/c/OpenJDK/jdk7/jdk/make/mkdemo/applets/ArcTest'

---

...
( cd c:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/CardTest && \
          C:/Progra~1/Java/jdk1.6.0_15/bin/jar -xfv CardTest.jar \
             -J-XX:-PrintVMOptions -J-XX:+UnlockDiagnosticVMOptions \
             -J-XX:-LogVMOutput -J-client -J-Xmx640m -J-Xms128m \
             -J-XX:PermSize=32m -J-XX:MaxPermSize=160m && \
          rm -f -r META-INF CardTest.jar && \
          if [ -w hotspot.log ] ; then rm -f hotspot.log; fi )
  created: META-INF/
 inflated: META-INF/MANIFEST.MF
 inflated: CardPanel.class
 inflated: CardTest.class
 inflated: example1.html
rm: cannot remove directory `META-INF': Directory not empty
make[6]: *** [bundles] Error 1
make[6]: Leaving directory `/cygdrive/c/OpenJDK/jdk7/jdk/make/mkdemo/applets/CardTest'

---

...
( cd
c:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/SimpleGraph && /usr/bin/unzip -o src.zip && rm -f src.zip )
Archive: src.zip
error: cannot create example1.html
  inflating: GraphApplet.java
make[6]: *** [bundles] Error 50
make[6]: Leaving directory
`/cygdrive/c/OpenJDK/jdk7/jdk/make/mkdemo/applets/SimpleGraph'

---

...
( cd c:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/Clock && \
          C:/Progra~1/Java/jdk1.6.0_15/bin/jar -xfv Clock.jar \
             -J-XX:-PrintVMOptions -J-XX:+UnlockDiagnosticVMOptions \
             -J-XX:-LogVMOutput -J-client -J-Xmx640m -J-Xms128m -J-XX:PermSize=32m \
             -J-XX:MaxPermSize=160m && \
          rm -f -r META-INF Clock.jar && \
          if [ -w hotspot.log ] ; then rm -f hotspot.log; fi )
  created: META-INF/
 inflated: META-INF/MANIFEST.MF
 inflated: Clock.class
 inflated: example1.html
Expanding source into demos area at c:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/Clock
( cd c:/OpenJDK/jdk7/build/windows-i586-fastdebug/demo/applets/Clock &&/usr/bin/unzip -o src.zip && rm -f src.zip )
Archive: src.zip
  inflating: Clock.java
error: cannot create example1.html
make[6]: *** [bundles] Error 50
make[6]: Leaving directory
`/cygdrive/c/OpenJDK/jdk7/jdk/make/mkdemo/applets/Clock'

---