File only visible to cygwin, not windows?

Question

Problem

We have a file created with keytool (from jdk 1.5) that is only visible with the ls command.
When we do a dir, it's not there.

Specifics

This file is owned by the user, all other files in the folder are owned by system.

The user is an administrator.

Hidden files and system files are set to visible in the explorer settings.

The file was created using the descriptions here: http://developer.android.com/guide/publishing/app-signing.html

$ keytool -genkey -v -keystore my-release-key.keystore

-alias alias_name -keyalg RSA -keysize 2048 -validity 10000

Output from dir command

C:\Program Files\Java\jdk1.5.0_22\bin>dir
 Volume in drive C is System
 Volume Serial Number is C0CC-F06B

 Directory of C:\Program Files\Java\jdk1.5.0_22\bin

2010-12-06  11:26    <DIR>          .
2010-12-06  11:26    <DIR>          ..
2009-10-09  02:36            53 370 appletviewer.exe
2009-10-09  02:36            53 359 apt.exe
2009-10-09  03:16            36 975 beanreg.dll
2009-10-09  02:36            53 368 extcheck.exe
2009-10-09  03:01            20 480 HtmlConverter.exe
2009-10-09  02:36            53 370 idlj.exe
2009-10-09  02:36            53 351 jar.exe
2009-10-09  02:36            53 372 jarsigner.exe
2009-10-09  02:36            53 344 java.exe
2009-10-09  02:36            53 365 javac.exe
2009-10-09  02:36            53 371 javadoc.exe
2009-10-09  02:36            53 365 javah.exe
2009-10-09  02:36            53 361 javap.exe
2009-10-09  02:36            53 346 javaw.exe
2009-10-09  03:01           131 174 javaws.exe
2009-10-09  02:36            53 370 jconsole.exe
2009-10-09  02:36            53 374 jdb.exe
2009-10-09  02:36            53 355 jps.exe
2009-10-09  02:36            53 361 jstat.exe
2009-10-09  02:36            53 364 jstatd.exe
2009-10-09  02:36            53 368 keytool.exe
2009-10-09  02:36            53 364 kinit.exe
2009-10-09  02:36            53 364 klist.exe
2009-10-09  02:36            53 362 ktab.exe
2009-10-09  02:36            53 382 native2ascii.exe
2009-10-09  02:36            53 383 orbd.exe
2009-10-09  02:36            53 376 pack200.exe
2009-10-09  03:01            69 745 packager.exe
2009-10-09  02:36            53 374 policytool.exe
2009-10-09  02:36            53 356 rmic.exe
2009-10-09  02:36            53 362 rmid.exe
2009-10-09  02:36            53 374 rmiregistry.exe
2009-10-09  02:36            53 373 serialver.exe
2009-10-09  02:36            53 395 servertool.exe
2009-10-09  02:36            53 392 tnameserv.exe
2009-10-09  02:36           127 101 unpack200.exe
              36 File(s)      2 039 866 bytes
               2 Dir(s)  12 419 006 464 bytes free

Output from cygwin ls command

C:\Program Files\Java\jdk1.5.0_22\bin>ls -l
total 2132
-rwx------+ 1 SYSTEM   SYSTEM        20480 Oct  9  2009 HtmlConverter.exe
-rwx------+ 1 SYSTEM   SYSTEM        53370 Oct  9  2009 appletviewer.exe
-rwx------+ 1 SYSTEM   SYSTEM        53359 Oct  9  2009 apt.exe
-rwx------+ 1 SYSTEM   SYSTEM        36975 Oct  9  2009 beanreg.dll
-rwx------+ 1 SYSTEM   SYSTEM        53368 Oct  9  2009 extcheck.exe
-rwx------+ 1 SYSTEM   SYSTEM        53370 Oct  9  2009 idlj.exe
-rwx------+ 1 SYSTEM   SYSTEM        53351 Oct  9  2009 jar.exe
-rwx------+ 1 SYSTEM   SYSTEM        53372 Oct  9  2009 jarsigner.exe
-rwx------+ 1 SYSTEM   SYSTEM        53344 Oct  9  2009 java.exe
-rwx------+ 1 SYSTEM   SYSTEM        53365 Oct  9  2009 javac.exe
-rwx------+ 1 SYSTEM   SYSTEM        53371 Oct  9  2009 javadoc.exe
-rwx------+ 1 SYSTEM   SYSTEM        53365 Oct  9  2009 javah.exe
-rwx------+ 1 SYSTEM   SYSTEM        53361 Oct  9  2009 javap.exe
-rwx------+ 1 SYSTEM   SYSTEM        53346 Oct  9  2009 javaw.exe
-rwx------+ 1 SYSTEM   SYSTEM       131174 Oct  9  2009 javaws.exe
-rwx------+ 1 SYSTEM   SYSTEM        53370 Oct  9  2009 jconsole.exe
-rwx------+ 1 SYSTEM   SYSTEM        53374 Oct  9  2009 jdb.exe
-rwx------+ 1 SYSTEM   SYSTEM        53355 Oct  9  2009 jps.exe
-rwx------+ 1 SYSTEM   SYSTEM        53361 Oct  9  2009 jstat.exe
-rwx------+ 1 SYSTEM   SYSTEM        53364 Oct  9  2009 jstatd.exe
-rwx------+ 1 SYSTEM   SYSTEM        53368 Oct  9  2009 keytool.exe
-rwx------+ 1 SYSTEM   SYSTEM        53364 Oct  9  2009 kinit.exe
-rwx------+ 1 SYSTEM   SYSTEM        53364 Oct  9  2009 klist.exe
-rwx------+ 1 SYSTEM   SYSTEM        53362 Oct  9  2009 ktab.exe
-rwx------+ 1 SYSTEM   SYSTEM        53382 Oct  9  2009 native2ascii.exe
-rwx------+ 1 SYSTEM   SYSTEM        53383 Oct  9  2009 orbd.exe
-rwx------+ 1 SYSTEM   SYSTEM        53376 Oct  9  2009 pack200.exe
-rwx------+ 1 SYSTEM   SYSTEM        69745 Oct  9  2009 packager.exe
-rwx------+ 1 SYSTEM   SYSTEM        53374 Oct  9  2009 policytool.exe
-rwx------+ 1 SYSTEM   SYSTEM        53356 Oct  9  2009 rmic.exe
-rwx------+ 1 SYSTEM   SYSTEM        53362 Oct  9  2009 rmid.exe
-rwx------+ 1 SYSTEM   SYSTEM        53374 Oct  9  2009 rmiregistry.exe
-rwx------+ 1 SYSTEM   SYSTEM        53373 Oct  9  2009 serialver.exe
-rwx------+ 1 SYSTEM   SYSTEM        53395 Oct  9  2009 servertool.exe
-rwx------+ 1 jchan    Domain Users   2207 Mar 14 11:51 key-android.jks
-rwx------+ 1 SYSTEM   SYSTEM        53392 Oct  9  2009 tnameserv.exe
-rwx------+ 1 SYSTEM   SYSTEM       127101 Oct  9  2009 unpack200.exe

Note the key-android.jks file that shows in the second listing.

Answer 1

On Windows Vista/7 the file is not under C:\Program Files\ but in the Virtualstore blow %localappdata%\VirtualStore\, as normal Users are not allowed to write in C:\Program Files\. Try to put the keyfile in another directory.

Answer 2

Check the access control lists on the file with the command cacls key-android.jks to see if the Administrator has access. Also check the ACL on the directory.