[Virtuous Ten Studio] ikjadoon:
You are TOO good at this stuff. Man, why doesn't Google hire you?! Thanks for the explanation! :D

A follow-up:

1) If ADB pull doesn't work, run VTS in administrator mode! :D

2) Deodexer works on *.jar files! :)

----

A slight issue. I tried the deodexer on android.policy.jar (some 330 bytes *.jar with a 800KB *.odex). Combined and compiled fine into a 335KB android.policy.jar. However, after I pushed it and deleted android.policy.odex and rebooted, I was stuck on a boot loop. :( If you're interested in looking, here is the log:

23:22:28.061: [Debug] - App.Application_Startup: 'Starting VTS'
23:22:28.071: [Debug] - VTSIPC.IsVTSAlreadyRunning: 'This is the only running VTS instance right now'
23:22:28.081: [Debug] - VTSIPC.StartServer: 'Creating VTS mutex'
23:22:28.081: [Debug] - VTSIPC.StartServer: 'Starting IPC server'
23:22:28.171: [Debug] - LicenseManager.GetLicense: 'Searching documents folder for license'
23:22:28.171: [Normal] - LicenseManager.GetLicense: 'No license file found, showing dialog'
23:22:28.221: [Debug] - RecentFilesViewModel.LoadRecentFilesFromSettings: 'Loading recent files, found 2'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'Problem loading assembly for version information: C:\Program Files (x86)\Virtuous Ten Studio\unins000.exe'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'VTS: 2.2.11.8210'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'LogFramework: 2.2.11.6802'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'SmaliStructure: 2.2.11.4496'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'M10Framework: 2.2.11.3620'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'M10Structure: 2.2.11.3028'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'Utilities: 2.2.11.4560'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'ToolWrapper: 2.2.11.6599'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'UACHelper: 2.2.11.4467'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'TaskFramework: 2.2.11.3365'
23:22:28.251: [Debug] - AboutViewModel.Initialize: 'SatisfactionTracker: 2.2.11.3449'
23:22:29.471: [Debug] - StartupManager.LogSystemInformation: 'OS: 6.1.7601.65536'
23:22:29.471: [Debug] - StartupManager.LogSystemInformation: '.Net: 4.0.30319.18034'
23:22:29.471: [Debug] - StartupManager.LogSystemInformation: 'CPU cores: 8'
23:22:29.471: [Debug] - StartupManager.LogSystemInformation: 'Resolution: 1920x1080'
23:22:29.471: [Debug] - StartupManager.LogSystemInformation: 'RAM: 8GB'
23:22:30.402: [Debug] - FileSystem.GetJavaInstallationPath: 'Found java path: C:\Program Files (x86)\Java\jre7\bin\java.exe'
23:22:30.402: [Debug] - ApkTool.ExecuteApkTool: 'ApkTool args: -version'
23:22:30.482: [Debug] - FileSystem.GetJavaInstallationPath: 'Found java path: C:\Program Files (x86)\Java\jre7\bin\java.exe'
23:22:30.482: [Debug] - ApkTool.ExecuteApkTool: 'ApkTool args: -version'
23:22:30.562: [Debug] - ApkTool.SearchForFrameworkPath: 'Using ApkTool framework path: C:\Users\Ibrahim Jadoon\apktool\framework'
23:22:31.236: [Debug] - SatisfactionLogger.UploadSatisfactionData: 'Upload successful!'
23:22:40.575: [Normal] - UpdateChecker.SearchForUpdates: 'Searching for updates, beta: True, alpha: False'
23:40:43.796: [Debug] - SmaliTool..cctor: 'Using smali binary: C:\Program Files (x86)\Virtuous Ten Studio\External\Smali\smali-1.4.1.jar'
23:40:43.796: [Debug] - SmaliTool..cctor: 'Using baksmali binary: C:\Program Files (x86)\Virtuous Ten Studio\External\Smali\baksmali-1.4.1.jar'
23:40:43.798: [Normal] - SmaliTool.Deodex: 'Deodexing file: C:\Program Files (x86)\Virtuous Ten Studio\External\ADB\Framework\android.policy.odex'
23:40:43.800: [Debug] - FileSystem.GetJavaInstallationPath: 'Found java path: C:\Program Files (x86)\Java\jre7\bin\java.exe'
23:40:43.800: [Debug] - SmaliTool.Deodex: 'Deodex args: -jar "C:\Program Files (x86)\Virtuous Ten Studio\External\Smali\baksmali-1.4.1.jar" --api-level 16 -x "C:\Program Files (x86)\Virtuous Ten Studio\External\ADB\Framework\android.policy.odex" -d "C:\Program Files (x86)\Virtuous Ten Studio\External\ADB\Framework" --output "C:\Users\Ibrahim Jadoon\AppData\Local\Temp\BB6133"'
23:40:47.080: [Debug] - SmaliTool.Deodex: 'Successfully deodexed file.'
23:40:47.082: [Normal] - SmaliTool.Smali: 'Compiling folder: C:\Users\Ibrahim Jadoon\AppData\Local\Temp\BB6133'
23:40:47.082: [Debug] - FileSystem.GetJavaInstallationPath: 'Found java path: C:\Program Files (x86)\Java\jre7\bin\java.exe'
23:40:47.082: [Debug] - SmaliTool.Smali: 'Smali args: -jar "C:\Program Files (x86)\Virtuous Ten Studio\External\Smali\smali-1.4.1.jar" --api-level 16 --output "C:\Users\Ibrahim Jadoon\AppData\Local\Temp\BB6133\classes.dex" "C:\Users\Ibrahim Jadoon\AppData\Local\Temp\BB6133"'
23:40:49.176: [Debug] - SmaliTool.Smali: 'Successfully compiled file.'

And attached is the android.policy.jar, if it matters (from an AT&T Galaxy S3, on 4.1.1 LK3).