[Mac developer build: 10/04/2016]
Please find the attachment for simple normal jar (com.greetings.jar)

Steps to reproduce

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JDK9 EXECUTION
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NOT WORKING SCENARIO

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STEP 1.
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 try to execute the following command at command line
javapackager -deploy -verbose -srcdir jars -srcfiles com.greetings.jar -BmainJar=com.greetings.jar -Bclasspath=com.greetings.jar -native dmg -outdir outdir -outfile test -BapplicationCategory=SomeCategory -name CategoryTestJDK9 -appclass com.greetings.App1

check the attachment log "categoryJDK9.txt" for successfull execution of javapackager command.

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STEP 2.
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install "dmg" file in mac using command
hdiutil attach /export/home/gtee/ramesh/outdir/CategoryTestJDK9-1.0.dmg

Checksumming Protective Master Boot Record (MBR : 0)…
Protective Master Boot Record (MBR :: verified CRC32 $AB890C57
Checksumming GPT Header (Primary GPT Header : 1)…
 GPT Header (Primary GPT Header : 1): verified CRC32 $22472931
Checksumming GPT Partition Data (Primary GPT Table : 2)…
GPT Partition Data (Primary GPT Tabl: verified CRC32 $CD1AE0EE
Checksumming (Apple_Free : 3)…
                    (Apple_Free : 3): verified CRC32 $00000000
Checksumming disk image (Apple_HFS : 4)…
...................................................................................................................................................................................................
          disk image (Apple_HFS : 4): verified CRC32 $7C08CB75
Checksumming (Apple_Free : 5)…
                    (Apple_Free : 5): verified CRC32 $00000000
Checksumming GPT Partition Data (Backup GPT Table : 6)…
GPT Partition Data (Backup GPT Table: verified CRC32 $CD1AE0EE
Checksumming GPT Header (Backup GPT Header : 7)…
  GPT Header (Backup GPT Header : 7): verified CRC32 $64D96B96
verified CRC32 $DFC4CC98
/dev/disk2 GUID_partition_scheme
/dev/disk2s1 Apple_HFS /Volumes/CategoryTestJDK9


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STEP 3.
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Check the Value of Key "LSApplicationCategoryType" in Info.plist
EXPECTED VALUE: SomeCategory (passed in jdk9 javapackager command line)
ACTUAL VALUE: public.app-category.developer-tools

cat /Volumes/CategoryTestJDK9/CategoryTestJDK9.app/Contents/Info.plist
<?xml version="1.0" ?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
 <dict>
  <key>LSMinimumSystemVersion</key>
  <string>10.7.4</string>
  <key>CFBundleDevelopmentRegion</key>
  <string>English</string>
  <key>CFBundleAllowMixedLocalizations</key>
  <true/>
  <key>CFBundleExecutable</key>
  <string>CategoryTestJDK9</string>
  <key>CFBundleIconFile</key>
  <string>CategoryTestJDK9.icns</string>
  <key>CFBundleIdentifier</key>
  <string>com.example.bad</string>
  <key>CFBundleInfoDictionaryVersion</key>
  <string>6.0</string>
  <key>CFBundleName</key>
  <string>CategoryTestJDK9</string>
  <key>CFBundlePackageType</key>
  <string>APPL</string>
  <key>CFBundleShortVersionString</key>
  <string>1.0</string>
  <key>CFBundleSignature</key>
  <string>????</string>
  <!-- See http://developer.apple.com/library/mac/#releasenotes/General/SubmittingToMacAppStore/_index.html
       for list of AppStore categories -->
  <key>LSApplicationCategoryType</key>
  <string>public.app-category.developer-tools</string>
  <key>CFBundleVersion</key>
  <string>1.0</string>
  <key>NSHumanReadableCopyright</key>
  <string>Copyright (C) 2016</string>
  <key>NSHighResolutionCapable</key>
  <string>true</string>
 </dict>
</plist>


Cross verified with JDK8 execution and "SomeCategory" value is observed for key "LSApplicationCategoryType" in Info.plist file
  

java -version
java version "1.8.0_122-ea"
Java(TM) SE Runtime Environment (build 1.8.0_122-ea-b01)
Java HotSpot(TM) 64-Bit Server VM (build 25.122-b01, mixed mode)

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JDK8 EXECUTION
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Repeat STEP 1, STEP 2, STEP 3 for JDK8 EXECUTION and you can observe value "SomeCategory" for Key "LsApplicatonCategoryType" in Info.plist


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STEP 4
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try the following command at command line with JDK8.

javapackager -deploy -verbose -srcdir jars -srcfiles com.greetings.jar -BmainJar=com.greetings.jar -Bclasspath=com.greetings.jar -native dmg -outdir outdir -outfile test -BapplicationCategory=SomeCategory -name CategoryTestJDK8 -appclass com.greetings.App1

Check the attachment "CategoryJDK8.txt" for successfull execution of JDK8 javapacakger command.

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STEP 5
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install bundler dmg file into mac system using following command line.

hdiutil attach /export/home/gtee/ramesh/outdir/bundles/CategoryTestJDK8-1.0.dmg

Checksumming Protective Master Boot Record (MBR : 0)…
Protective Master Boot Record (MBR :: verified CRC32 $A731BE91
Checksumming GPT Header (Primary GPT Header : 1)…
 GPT Header (Primary GPT Header : 1): verified CRC32 $6A3D23B7
Checksumming GPT Partition Data (Primary GPT Table : 2)…
GPT Partition Data (Primary GPT Tabl: verified CRC32 $844BF4CC
Checksumming (Apple_Free : 3)…
                    (Apple_Free : 3): verified CRC32 $00000000
Checksumming disk image (Apple_HFS : 4)…
...................................................................................................................................................................................................
          disk image (Apple_HFS : 4): verified CRC32 $680682C3
Checksumming (Apple_Free : 5)…
                    (Apple_Free : 5): verified CRC32 $00000000
Checksumming GPT Partition Data (Backup GPT Table : 6)…
GPT Partition Data (Backup GPT Table: verified CRC32 $844BF4CC
Checksumming GPT Header (Backup GPT Header : 7)…
  GPT Header (Backup GPT Header : 7): verified CRC32 $9AF1B4DB
verified CRC32 $33805036
/dev/disk3 GUID_partition_scheme
/dev/disk3s1 Apple_HFS /Volumes/CategoryTestJDK8

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STEP 6
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check the value for key "LSApplicationCategoryType" in Info.plist

 cat /Volumes/CategoryTestJDK8/CategoryTestJDK8.app/Contents/Info.plist
<?xml version="1.0" ?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
 <dict>
  <key>LSMinimumSystemVersion</key>
  <string>10.7.4</string>
  <key>CFBundleDevelopmentRegion</key>
  <string>English</string>
  <key>CFBundleAllowMixedLocalizations</key>
  <true/>
  <key>CFBundleExecutable</key>
  <string>CategoryTestJDK8</string>
  <key>CFBundleIconFile</key>
  <string>CategoryTestJDK8.icns</string>
  <key>CFBundleIdentifier</key>
  <string>com.greetings</string>
  <key>CFBundleInfoDictionaryVersion</key>
  <string>6.0</string>
  <key>CFBundleName</key>
  <string>CategoryTestJDK8</string>
  <key>CFBundlePackageType</key>
  <string>APPL</string>
  <key>CFBundleShortVersionString</key>
  <string>1.0</string>
  <key>CFBundleSignature</key>
  <string>????</string>
  <!-- See http://developer.apple.com/library/mac/#releasenotes/General/SubmittingToMacAppStore/_index.html
       for list of AppStore categories -->
  <key>LSApplicationCategoryType</key>
  <string>SomeCategory</string>
  <key>CFBundleVersion</key>
  <string>1.0</string>
  <key>NSHumanReadableCopyright</key>
  <string>Copyright (C) 2016</string>
  <key>NSHighResolutionCapable</key>
  <string>true</string>
 </dict>
</plist>