TYPO3 Core

Tom, can you please take a look at this.

<?php
# PackageStates.php

# This file is maintained by Flow's package management. Although you can edit it
# manually, you should rather use the command line commands for maintaining packages.
# You'll find detailed information about the typo3.flow:package:* commands in their
# respective help screens.

# This file will be regenerated automatically if it doesn't exist. Deleting this file
# should, however, never become necessary if you use the package commands.

return array (
  'packages' => 
  array (
    'core' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/core',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/core/',
      'classesPath' => 'Classes/',
    ),
    'sys_note' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/sys-note',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/sys_note/',
      'classesPath' => 'Classes/',
    ),
    'backend' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/backend',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/backend/',
      'classesPath' => 'Classes/',
    ),
    'tstemplate' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/tstemplate',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/tstemplate/',
      'classesPath' => 'Classes/',
    ),
    'viewpage' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/viewpage',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/viewpage/',
      'classesPath' => 'Classes/',
    ),
    'felogin' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/felogin',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/felogin/',
      'classesPath' => 'Classes/',
    ),
    'func_wizards' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/func-wizards',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/func_wizards/',
      'classesPath' => 'Classes/',
    ),
    'rtehtmlarea' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/rtehtmlarea',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/rtehtmlarea/',
      'classesPath' => 'Classes/',
    ),
    'aboutmodules' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/aboutmodules',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/aboutmodules/',
      'classesPath' => 'Classes/',
    ),
    'form' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/form',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/form/',
      'classesPath' => 'Classes/',
    ),
    'filelist' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/filelist',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/filelist/',
      'classesPath' => 'Classes/',
    ),
    'sv' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/sv',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/sv/',
      'classesPath' => 'Classes/',
    ),
    'info_pagetsconfig' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/info-pagetsconfig',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/info_pagetsconfig/',
      'classesPath' => 'Classes/',
    ),
    't3editor' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/t3editor',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/t3editor/',
      'classesPath' => 'Classes/',
    ),
    'belog' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/belog',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/belog/',
      'classesPath' => 'Classes/',
    ),
    'func' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/func',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/func/',
      'classesPath' => 'Classes/',
    ),
    'context_help' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/context-help',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/context_help/',
      'classesPath' => 'Classes/',
    ),
    'lowlevel' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/lowlevel',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/lowlevel/',
      'classesPath' => 'Classes/',
    ),
    'cshmanual' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/cshmanual',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/cshmanual/',
      'classesPath' => 'Classes/',
    ),
    'reports' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/reports',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/reports/',
      'classesPath' => 'Classes/',
    ),
    'info' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/info',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/info/',
      'classesPath' => 'Classes/',
    ),
    'setup' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/setup',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/setup/',
      'classesPath' => 'Classes/',
    ),
    'perm' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/perm',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/perm/',
      'classesPath' => 'Classes/',
    ),
    'beuser' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/beuser',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/beuser/',
      'classesPath' => 'Classes/',
    ),
    'recordlist' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/recordlist',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/recordlist/',
      'classesPath' => 'Classes/',
    ),
    'fluid' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/fluid',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/fluid/',
      'classesPath' => 'Classes/',
    ),
    'extbase' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/extbase',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/extbase/',
      'classesPath' => 'Classes/',
    ),
    'install' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/install',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/install/',
      'classesPath' => 'Classes/',
    ),
    'about' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/about',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/about/',
      'classesPath' => 'Classes/',
    ),
    'extensionmanager' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/extensionmanager',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/extensionmanager/',
      'classesPath' => 'Classes/',
    ),
    'cms' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/cms',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/cms/',
      'classesPath' => 'Classes/',
    ),
    'frontend' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/frontend',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/frontend/',
      'classesPath' => 'Classes/',
    ),
    'rsaauth' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/rsaauth',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/rsaauth/',
      'classesPath' => 'Classes/',
    ),
    'wizard_crpages' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/wizard-crpages',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/wizard_crpages/',
      'classesPath' => 'Classes/',
    ),
    'documentation' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/documentation',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/documentation/',
      'classesPath' => 'Classes/',
    ),
    't3skin' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/t3skin',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/t3skin/',
      'classesPath' => 'Classes/',
    ),
    'impexp' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/impexp',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/impexp/',
      'classesPath' => 'Classes/',
    ),
    'extra_page_cm_options' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/extra-page-cm-options',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/extra_page_cm_options/',
      'classesPath' => 'Classes/',
    ),
    'wizard_sortpages' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/wizard-sortpages',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/wizard_sortpages/',
      'classesPath' => 'Classes/',
    ),
    'saltedpasswords' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/saltedpasswords',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/saltedpasswords/',
      'classesPath' => 'Classes/',
    ),
    'lang' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/lang',
      'state' => 'active',
      'packagePath' => 'typo3/sysext/lang/',
      'classesPath' => 'Classes/',
    ),
    'adodb' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/adodb',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/adodb/',
      'classesPath' => 'Classes/',
    ),
    'linkvalidator' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/linkvalidator',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/linkvalidator/',
      'classesPath' => 'Classes/',
    ),
    'feedit' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/feedit',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/feedit/',
      'classesPath' => 'Classes/',
    ),
    'opendocs' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/opendocs',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/opendocs/',
      'classesPath' => 'Classes/',
    ),
    'openid' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/openid',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/openid/',
      'classesPath' => 'Classes/',
    ),
    'workspaces' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/workspaces',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/workspaces/',
      'classesPath' => 'Classes/',
    ),
    'filemetadata' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/filemetadata',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/filemetadata/',
      'classesPath' => 'Classes/',
    ),
    'indexed_search_mysql' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/indexed-search-mysql',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/indexed_search_mysql/',
      'classesPath' => 'Classes/',
    ),
    'css_styled_content' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/css-styled-content',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/css_styled_content/',
      'classesPath' => 'Classes/',
    ),
    'sys_action' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/sys-action',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/sys_action/',
      'classesPath' => 'Classes/',
    ),
    'taskcenter' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/taskcenter',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/taskcenter/',
      'classesPath' => 'Classes/',
    ),
    'version' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/version',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/version/',
      'classesPath' => 'Classes/',
    ),
    'recycler' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/recycler',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/recycler/',
      'classesPath' => 'Classes/',
    ),
    'indexed_search' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/indexed-search',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/indexed_search/',
      'classesPath' => 'Classes/',
    ),
    'dbal' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/dbal',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/dbal/',
      'classesPath' => 'Classes/',
    ),
    'scheduler' => 
    array (
      'manifestPath' => '',
      'composerName' => 'typo3/cms/scheduler',
      'state' => 'inactive',
      'packagePath' => 'typo3/sysext/scheduler/',
      'classesPath' => 'Classes/',
    ),
  ),
  'version' => 4,
)
 ?>

Here´s the command executed¶

web1@RSYSTEM1:~/html/subdomains/playground_62$ ls -la
insgesamt 40
drwxr-xr-x  8 web1 web1 4096 17. Feb 12:57 .
drwxr-xr-x 31 web1 web1 4096 17. Feb 05:22 ..
drwxr-xr-x  3 web1 web1 4096 17. Feb 05:22 8714035
drwxr-xr-x  4 web1 web1 4096 17. Feb 08:15 fileadmin
lrwxrwxrwx  1 web1 web1   19 17. Feb 05:24 index.php -> typo3_src/index.php
-rw-r--r--  1 web1 web1 2345 17. Feb 07:44 install_typo3_62_ft3.sh
-rwxr-xr-x  1 web1 web1 2341 17. Feb 12:57 install_typo3_62_ft3.sh.save
lrwxrwxrwx  1 web1 web1   15 17. Feb 05:24 typo3 -> typo3_src/typo3
drwxr-xr-x  5 web1 web1 4096 17. Feb 07:45 TYPO3.CMS
drwxr-xr-x  4 web1 web1 4096 20. Feb 16:00 typo3conf
lrwxrwxrwx  1 web1 web1    9 17. Feb 05:24 typo3_src -> TYPO3.CMS
drwxr-xr-x 14 web1 web1 4096 17. Feb 08:15 typo3temp
drwxr-xr-x  5 web1 web1 4096 17. Feb 08:15 uploads
web1@RSYSTEM1:~/html/subdomains/playground_62$ 

This is the typo3conf Folder¶

web1@RSYSTEM1:~/html/subdomains/playground_62/typo3conf$ ls -la
insgesamt 52
drwxr-xr-x 4 web1 web1  4096 20. Feb 16:00 .
drwxr-xr-x 8 web1 web1  4096 17. Feb 12:57 ..
-rw-r--r-- 1 web1 web1     0 17. Feb 08:15 ENABLE_INSTALL_TOOL
drwxr-xr-x 8 web1 web1  4096 17. Feb 08:15 ext
drwxr-xr-x 2 web1 web1  4096 17. Feb 08:15 l10n
-rw-r--r-- 1 web1 web1  2734 17. Feb 07:26 LocalConfiguration.php
-rw-r--r-- 1 web1 web1 13428 17. Feb 06:56 PackageStates.php
-rw-r--r-- 1 web1 web1 13428 20. Feb 16:00 PackageStates.txt
web1@RSYSTEM1:~/html/subdomains/playground_62/typo3conf$ 

This System needs to run everything on 644 and 755 permissions

Here´s the LocalConfiguration.php¶

<?php
return array(
    'BE' => array(
        'compressionLevel' => '5',
        'debug' => '1',
        'disable_exec_function' => '0',
        'explicitADmode' => 'explicitAllow',
        'fileCreateMask' => '0644',
        'flexformForceCDATA' => '1',
        'folderCreateMask' => '0755',
        'installToolPassword' => 'not',
        'loginSecurityLevel' => 'rsa',
        'maxFileSize' => '2502400',
        'sessionTimeout' => '7200',
        'versionNumberInFilename' => '0',
        'warning_email_addr' => 'yep',
        'warning_mode' => '2',
    ),
    'DB' => array(
        'database' => 'usr_web1_25',
        'extTablesDefinitionScript' => 'extTables.php',
        'host' => 'localhost',
        'password' => 'pass',
        'port' => 3306,
        'socket' => '',
        'username' => 'web1',
    ),
    'EXT' => array(
        'extConf' => array(
            'rsaauth' => 'a:1:{s:18:"temporaryDirectory";s:0:"";}',
            'saltedpasswords' => 'a:2:{s:3:"BE.";a:4:{s:21:"saltedPWHashingMethod";s:41:"TYPO3\\CMS\\Saltedpasswords\\Salt\\PhpassSalt";s:11:"forceSalted";i:0;s:15:"onlyAuthService";i:0;s:12:"updatePasswd";i:1;}s:3:"FE.";a:5:{s:7:"enabled";i:1;s:21:"saltedPWHashingMethod";s:41:"TYPO3\\CMS\\Saltedpasswords\\Salt\\PhpassSalt";s:11:"forceSalted";i:0;s:15:"onlyAuthService";i:0;s:12:"updatePasswd";i:1;}}',
        ),
    ),
    'FE' => array(
        'debug' => '0',
        'loginSecurityLevel' => 'rsa',
    ),
    'GFX' => array(
        'TTFdpi' => '96',
        'colorspace' => 'RGB',
        'gdlib_png' => '1',
        'im' => '1',
        'im_mask_temp_ext_gif' => '1',
        'im_path' => '/usr/local/bin/',
        'im_path_lzw' => '/usr/local/bin/',
        'im_v5effects' => '-1',
        'im_version_5' => 'gm',
        'image_processing' => '1',
        'jpg_quality' => '100',
        'png_truecolor' => '1',
        'thumbnails_png' => '1',
    ),
    'SYS' => array(
        'UTF8filesystem' => '1',
        'binPath' => '/usr/local/bin',
        'caching' => array(
            'cacheConfigurations' => array(
                'extbase_object' => array(),
            ),
        ),
        'compat_version' => '6.2',
        'curlUse' => '1',
        'ddmmyy' => 'd-m-y',
        'debugExceptionHandler' => 't3lib_error_DebugExceptionHandler',
        'devIPmask' => '127.0.0.1,',
        'displayErrors' => '1',
        'enableDeprecationLog' => '0',
        'enable_errorDLOG' => '0',
        'enable_exceptionDLOG' => '0',
        'encryptionKey' => 'foo',
        'errorHandler' => 't3lib_error_ErrorHandler',
        'isInitialInstallationInProgress' => FALSE,
        'maxFileNameLength' => '90',
        'phpTimeZone' => 'Europe/Berlin',
        'productionExceptionHandler' => 't3lib_error_DebugExceptionHandler',
        'sitename' => 'Playground62',
        'sqlDebug' => '1',
        'systemLocale' => 'de_DE.utf-8',
        'systemLog' => 'error_log',
        'systemLogLevel' => '0',
        't3lib_cs_convMethod' => 'mbstring',
        't3lib_cs_utils' => 'mbstring',
    ),
);
?>

I just applied your PackageStates file and Localconf to some installs at mine. It does simply work. This is really strange.

Could you please execute the following command in the directory of your site and give me the output?

php -r "var_dump(include('typo3conf/PackageStates.php') ?: array());" 

The Output¶

array(2) {
  ["packages"]=>
  array(57) {
    ["core"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(14) "typo3/cms/core" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(18) "typo3/sysext/core/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["sys_note"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(18) "typo3/cms/sys-note" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(22) "typo3/sysext/sys_note/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["backend"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(17) "typo3/cms/backend" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(21) "typo3/sysext/backend/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["tstemplate"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(20) "typo3/cms/tstemplate" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(24) "typo3/sysext/tstemplate/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["viewpage"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(18) "typo3/cms/viewpage" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(22) "typo3/sysext/viewpage/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["felogin"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(17) "typo3/cms/felogin" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(21) "typo3/sysext/felogin/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["func_wizards"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(22) "typo3/cms/func-wizards" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(26) "typo3/sysext/func_wizards/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["rtehtmlarea"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(21) "typo3/cms/rtehtmlarea" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(25) "typo3/sysext/rtehtmlarea/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["aboutmodules"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(22) "typo3/cms/aboutmodules" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(26) "typo3/sysext/aboutmodules/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["form"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(14) "typo3/cms/form" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(18) "typo3/sysext/form/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["filelist"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(18) "typo3/cms/filelist" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(22) "typo3/sysext/filelist/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["sv"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(12) "typo3/cms/sv" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(16) "typo3/sysext/sv/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["info_pagetsconfig"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(27) "typo3/cms/info-pagetsconfig" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(31) "typo3/sysext/info_pagetsconfig/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["t3editor"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(18) "typo3/cms/t3editor" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(22) "typo3/sysext/t3editor/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["belog"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(15) "typo3/cms/belog" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(19) "typo3/sysext/belog/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["func"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(14) "typo3/cms/func" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(18) "typo3/sysext/func/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["context_help"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(22) "typo3/cms/context-help" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(26) "typo3/sysext/context_help/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["lowlevel"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(18) "typo3/cms/lowlevel" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(22) "typo3/sysext/lowlevel/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["cshmanual"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(19) "typo3/cms/cshmanual" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(23) "typo3/sysext/cshmanual/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["reports"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(17) "typo3/cms/reports" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(21) "typo3/sysext/reports/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["info"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(14) "typo3/cms/info" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(18) "typo3/sysext/info/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["setup"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(15) "typo3/cms/setup" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(19) "typo3/sysext/setup/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["perm"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(14) "typo3/cms/perm" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(18) "typo3/sysext/perm/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["beuser"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(16) "typo3/cms/beuser" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(20) "typo3/sysext/beuser/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["recordlist"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(20) "typo3/cms/recordlist" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(24) "typo3/sysext/recordlist/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["fluid"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(15) "typo3/cms/fluid" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(19) "typo3/sysext/fluid/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["extbase"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(17) "typo3/cms/extbase" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(21) "typo3/sysext/extbase/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["install"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(17) "typo3/cms/install" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(21) "typo3/sysext/install/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["about"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(15) "typo3/cms/about" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(19) "typo3/sysext/about/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["extensionmanager"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(26) "typo3/cms/extensionmanager" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(30) "typo3/sysext/extensionmanager/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["cms"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(13) "typo3/cms/cms" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(17) "typo3/sysext/cms/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["frontend"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(18) "typo3/cms/frontend" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(22) "typo3/sysext/frontend/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["rsaauth"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(17) "typo3/cms/rsaauth" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(21) "typo3/sysext/rsaauth/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["wizard_crpages"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(24) "typo3/cms/wizard-crpages" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(28) "typo3/sysext/wizard_crpages/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["documentation"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(23) "typo3/cms/documentation" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(27) "typo3/sysext/documentation/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["t3skin"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(16) "typo3/cms/t3skin" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(20) "typo3/sysext/t3skin/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["impexp"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(16) "typo3/cms/impexp" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(20) "typo3/sysext/impexp/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["extra_page_cm_options"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(31) "typo3/cms/extra-page-cm-options" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(35) "typo3/sysext/extra_page_cm_options/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["wizard_sortpages"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(26) "typo3/cms/wizard-sortpages" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(30) "typo3/sysext/wizard_sortpages/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["saltedpasswords"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(25) "typo3/cms/saltedpasswords" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(29) "typo3/sysext/saltedpasswords/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["lang"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(14) "typo3/cms/lang" 
      ["state"]=>
      string(6) "active" 
      ["packagePath"]=>
      string(18) "typo3/sysext/lang/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["adodb"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(15) "typo3/cms/adodb" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(19) "typo3/sysext/adodb/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["linkvalidator"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(23) "typo3/cms/linkvalidator" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(27) "typo3/sysext/linkvalidator/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["feedit"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(16) "typo3/cms/feedit" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(20) "typo3/sysext/feedit/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["opendocs"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(18) "typo3/cms/opendocs" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(22) "typo3/sysext/opendocs/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["openid"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(16) "typo3/cms/openid" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(20) "typo3/sysext/openid/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["workspaces"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(20) "typo3/cms/workspaces" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(24) "typo3/sysext/workspaces/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["filemetadata"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(22) "typo3/cms/filemetadata" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(26) "typo3/sysext/filemetadata/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["indexed_search_mysql"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(30) "typo3/cms/indexed-search-mysql" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(34) "typo3/sysext/indexed_search_mysql/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["css_styled_content"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(28) "typo3/cms/css-styled-content" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(32) "typo3/sysext/css_styled_content/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["sys_action"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(20) "typo3/cms/sys-action" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(24) "typo3/sysext/sys_action/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["taskcenter"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(20) "typo3/cms/taskcenter" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(24) "typo3/sysext/taskcenter/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["version"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(17) "typo3/cms/version" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(21) "typo3/sysext/version/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["recycler"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(18) "typo3/cms/recycler" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(22) "typo3/sysext/recycler/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["indexed_search"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(24) "typo3/cms/indexed-search" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(28) "typo3/sysext/indexed_search/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["dbal"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(14) "typo3/cms/dbal" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(18) "typo3/sysext/dbal/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
    ["scheduler"]=>
    array(5) {
      ["manifestPath"]=>
      string(0) "" 
      ["composerName"]=>
      string(19) "typo3/cms/scheduler" 
      ["state"]=>
      string(8) "inactive" 
      ["packagePath"]=>
      string(23) "typo3/sysext/scheduler/" 
      ["classesPath"]=>
      string(8) "Classes/" 
    }
  }
  ["version"]=>
  int(4)
}

Everything seems fine. Something goes really wrong.

Look at the following code from the PackageManager L236-244

            $this->packageStatesConfiguration = @include($this->packageStatesPathAndFilename) ?: array();
            if (!isset($this->packageStatesConfiguration['version']) || $this->packageStatesConfiguration['version'] < 4) {
                $this->packageStatesConfiguration = array();
            }
            if ($this->packageStatesConfiguration !== array()) {
                $this->registerPackagesFromConfiguration();
            } else {
                throw new Exception\PackageStatesUnavailableException('The PackageStates.php file is either corrupt or unavailable.', 1381507733);
            }

According to the output you've given me in the above comments the version key is set up properly.

So the only way this could go wrong is if the @include returns some garbage.

If you have APC installed a reason for this could be that "apc.include_once_override" is switched off. You can verify this by executing

php -i | grep apc.include_once_override

This can cause some bugs. Another story is the flag "apc.stat", that is switched off. An empty PackageStates.php files has been cached then beforehand and is continuously returned.

No, no APC - here complete PHP config¶

phpinfo()
PHP Version => 5.4.25

System => Linux RSYSTEM1 2.6.32-5-amd64 #1 SMP Mon Sep 23 22:14:43 UTC 2013 x86_64
Build Date => Feb 19 2014 07:19:27
Configure Command =>  './configure'  '--sysconfdir=/etc/php5.4' '--bindir=/usr/local/bin/php54' '--with-zlib' '--with-zend-multibyte' '--enable-mbstring' '--with-bz2' '--with-openssl' '--enable-zip' '--enable-soap' '--with-curl' '--with-gettext' '--with-mcrypt' '--with-mhash' '--with-xmlrpc' '--with-xsl' '--with-mysql' '--with-mysqli' '--with-pdo-odbc=unixODBC,/usr' '--with-gd' '--enable-gd-native-ttf' '--with-freetype-dir' '--with-config-file-scan-dir=/etc/php5.4/conf.d/' '--with-pdo-mysql' '--with-jpeg-dir=/usr'
Server API => Command Line Interface
Virtual Directory Support => disabled
Configuration File (php.ini) Path => /usr/local/lib
Loaded Configuration File => (none)
Scan this dir for additional .ini files => /etc/php5.4/conf.d/
Additional .ini files parsed => /etc/php5.4/conf.d/ioncube.ini,
/etc/php5.4/conf.d/pdo_odbc.ini

PHP API => 20100412
PHP Extension => 20100525
Zend Extension => 220100525
Zend Extension Build => API220100525,NTS
PHP Extension Build => API20100525,NTS
Debug Build => no
Thread Safety => disabled
Zend Signal Handling => disabled
Zend Memory Manager => enabled
Zend Multibyte Support => provided by mbstring
IPv6 Support => enabled
DTrace Support => disabled

Registered PHP Streams => https, ftps, compress.zlib, compress.bzip2, php, file, glob, data, http, ftp, phar, zip
Registered Stream Socket Transports => tcp, udp, unix, udg, ssl, sslv3, sslv2, tls
Registered Stream Filters => zlib.*, bzip2.*, convert.iconv.*, mcrypt.*, mdecrypt.*, string.rot13, string.toupper, string.tolower, string.strip_tags, convert.*, consumed, dechunk

This program makes use of the Zend Scripting Language Engine:
Zend Engine v2.4.0, Copyright (c) 1998-2014 Zend Technologies
    with the ionCube PHP Loader v4.2.2, Copyright (c) 2002-2012, by ionCube Ltd.

 _______________________________________________________________________

Configuration

bz2

BZip2 Support => Enabled
Stream Wrapper support => compress.bzip2://
Stream Filter support => bzip2.decompress, bzip2.compress
BZip2 Version => 1.0.5, 10-Dec-2007

Core

PHP Version => 5.4.25

Directive => Local Value => Master Value
allow_url_fopen => On => On
allow_url_include => Off => Off
always_populate_raw_post_data => Off => Off
arg_separator.input => & => &
arg_separator.output => & => &
asp_tags => Off => Off
auto_append_file => no value => no value
auto_globals_jit => On => On
auto_prepend_file => no value => no value
browscap => no value => no value
default_charset => no value => no value
default_mimetype => text/html => text/html
disable_classes => no value => no value
disable_functions => no value => no value
display_errors => STDOUT => STDOUT
display_startup_errors => Off => Off
doc_root => no value => no value
docref_ext => no value => no value
docref_root => no value => no value
enable_dl => On => On
enable_post_data_reading => On => On
error_append_string => no value => no value
error_log => no value => no value
error_prepend_string => no value => no value
error_reporting => no value => no value
exit_on_timeout => Off => Off
expose_php => On => On
extension_dir => /usr/local/lib/php/extensions/no-debug-non-zts-20100525 => /usr/local/lib/php/extensions/no-debug-non-zts-20100525
file_uploads => On => On
highlight.comment => <font style="color: #FF8000">#FF8000</font> => <font style="color: #FF8000">#FF8000</font>
highlight.default => <font style="color: #0000BB">#0000BB</font> => <font style="color: #0000BB">#0000BB</font>
highlight.html => <font style="color: #000000">#000000</font> => <font style="color: #000000">#000000</font>
highlight.keyword => <font style="color: #007700">#007700</font> => <font style="color: #007700">#007700</font>
highlight.string => <font style="color: #DD0000">#DD0000</font> => <font style="color: #DD0000">#DD0000</font>
html_errors => Off => Off
ignore_repeated_errors => Off => Off
ignore_repeated_source => Off => Off
ignore_user_abort => Off => Off
implicit_flush => On => On
include_path => .:/usr/local/lib/php => .:/usr/local/lib/php
log_errors => Off => Off
log_errors_max_len => 1024 => 1024
mail.add_x_header => Off => Off
mail.force_extra_parameters => no value => no value
mail.log => no value => no value
max_execution_time => 0 => 0
max_file_uploads => 20 => 20
max_input_nesting_level => 64 => 64
max_input_time => -1 => -1
max_input_vars => 1000 => 1000
memory_limit => 128M => 128M
open_basedir => no value => no value
output_buffering => 0 => 0
output_handler => no value => no value
post_max_size => 8M => 8M
precision => 14 => 14
realpath_cache_size => 16K => 16K
realpath_cache_ttl => 120 => 120
register_argc_argv => On => On
report_memleaks => On => On
report_zend_debug => Off => Off
request_order => no value => no value
sendmail_from => no value => no value
sendmail_path => /usr/sbin/sendmail -t -i  => /usr/sbin/sendmail -t -i 
serialize_precision => 17 => 17
short_open_tag => On => On
SMTP => localhost => localhost
smtp_port => 25 => 25
sql.safe_mode => Off => Off
track_errors => Off => Off
unserialize_callback_func => no value => no value
upload_max_filesize => 2M => 2M
upload_tmp_dir => no value => no value
user_dir => no value => no value
user_ini.cache_ttl => 300 => 300
user_ini.filename => .user.ini => .user.ini
variables_order => EGPCS => EGPCS
xmlrpc_error_number => 0 => 0
xmlrpc_errors => Off => Off
zend.detect_unicode => On => On
zend.enable_gc => On => On
zend.multibyte => Off => Off
zend.script_encoding => no value => no value

ctype

ctype functions => enabled

curl

cURL support => enabled
cURL Information => 7.21.0
Age => 3
Features
AsynchDNS => No
Debug => No
GSS-Negotiate => Yes
IDN => Yes
IPv6 => Yes
Largefile => Yes
NTLM => Yes
SPNEGO => No
SSL => Yes
SSPI => No
krb4 => No
libz => Yes
CharConv => No
Protocols => dict, file, ftp, ftps, http, https, imap, imaps, ldap, ldaps, pop3, pop3s, rtsp, scp, sftp, smtp, smtps, telnet, tftp
Host => x86_64-pc-linux-gnu
SSL Version => OpenSSL/0.9.8o
ZLib Version => 1.2.3.4
libSSH Version => libssh2/1.2.6

date

date/time support => enabled
"Olson" Timezone Database Version => 2013.9
Timezone Database => internal
Default timezone => UTC

Directive => Local Value => Master Value
date.default_latitude => 31.7667 => 31.7667
date.default_longitude => 35.2333 => 35.2333
date.sunrise_zenith => 90.583333 => 90.583333
date.sunset_zenith => 90.583333 => 90.583333
date.timezone => no value => no value

dom

DOM/XML => enabled
DOM/XML API Version => 20031129
libxml Version => 2.7.8
HTML Support => enabled
XPath Support => enabled
XPointer Support => enabled
Schema Support => enabled
RelaxNG Support => enabled

ereg

Regex Library => Bundled library enabled

fileinfo

fileinfo support => enabled
version => 1.0.5

filter

Input Validation and Filtering => enabled
Revision => $Id: ad78b4a085153b8c7f4d6db5dc69df40e969c343 $

Directive => Local Value => Master Value
filter.default => unsafe_raw => unsafe_raw
filter.default_flags => no value => no value

gd

GD Support => enabled
GD Version => bundled (2.1.0 compatible)
FreeType Support => enabled
FreeType Linkage => with freetype
FreeType Version => 2.4.2
GIF Read Support => enabled
GIF Create Support => enabled
JPEG Support => enabled
libJPEG Version => 6b
PNG Support => enabled
libPNG Version => 1.2.44
WBMP Support => enabled
XBM Support => enabled

Directive => Local Value => Master Value
gd.jpeg_ignore_warning => 0 => 0

gettext

GetText Support => enabled

hash

hash support => enabled
Hashing Engines => md2 md4 md5 sha1 sha224 sha256 sha384 sha512 ripemd128 ripemd160 ripemd256 ripemd320 whirlpool tiger128,3 tiger160,3 tiger192,3 tiger128,4 tiger160,4 tiger192,4 snefru snefru256 gost adler32 crc32 crc32b fnv132 fnv164 joaat haval128,3 haval160,3 haval192,3 haval224,3 haval256,3 haval128,4 haval160,4 haval192,4 haval224,4 haval256,4 haval128,5 haval160,5 haval192,5 haval224,5 haval256,5 

iconv

iconv support => enabled
iconv implementation => glibc
iconv library version => 2.11.3

Directive => Local Value => Master Value
iconv.input_encoding => ISO-8859-1 => ISO-8859-1
iconv.internal_encoding => ISO-8859-1 => ISO-8859-1
iconv.output_encoding => ISO-8859-1 => ISO-8859-1

json

json support => enabled
json version => 1.2.1

libxml

libXML support => active
libXML Compiled Version => 2.7.8
libXML Loaded Version => 20708
libXML streams => enabled

mbstring

Multibyte Support => enabled
Multibyte string engine => libmbfl
HTTP input encoding translation => disabled
libmbfl version => 1.3.2

mbstring extension makes use of "streamable kanji code filter and converter", which is distributed under the GNU Lesser General Public License version 2.1.

Multibyte (japanese) regex support => enabled
Multibyte regex (oniguruma) backtrack check => On
Multibyte regex (oniguruma) version => 4.7.1

Directive => Local Value => Master Value
mbstring.detect_order => no value => no value
mbstring.encoding_translation => Off => Off
mbstring.func_overload => 0 => 0
mbstring.http_input => pass => pass
mbstring.http_output => pass => pass
mbstring.http_output_conv_mimetypes => ^(text/|application/xhtml\+xml) => ^(text/|application/xhtml\+xml)
mbstring.internal_encoding => no value => no value
mbstring.language => neutral => neutral
mbstring.strict_detection => Off => Off
mbstring.substitute_character => no value => no value

mcrypt

mcrypt support => enabled
mcrypt_filter support => enabled
Version => 2.5.8
Api No => 20021217
Supported ciphers => cast-128 gost rijndael-128 twofish arcfour cast-256 loki97 rijndael-192 saferplus wake blowfish-compat des rijndael-256 serpent xtea blowfish enigma rc2 tripledes 
Supported modes => cbc cfb ctr ecb ncfb nofb ofb stream 

Directive => Local Value => Master Value
mcrypt.algorithms_dir => no value => no value
mcrypt.modes_dir => no value => no value

mhash

MHASH support => Enabled
MHASH API Version => Emulated Support

mysql

MySQL Support => enabled
Active Persistent Links => 0
Active Links => 0
Client API version => mysqlnd 5.0.10 - 20111026 - $Id: c85105d7c6f7d70d609bb4c000257868a40840ab $

Directive => Local Value => Master Value
mysql.allow_local_infile => On => On
mysql.allow_persistent => On => On
mysql.connect_timeout => 60 => 60
mysql.default_host => no value => no value
mysql.default_password => no value => no value
mysql.default_port => no value => no value
mysql.default_socket => /var/run/mysqld/mysqld.sock => /var/run/mysqld/mysqld.sock
mysql.default_user => no value => no value
mysql.max_links => Unlimited => Unlimited
mysql.max_persistent => Unlimited => Unlimited
mysql.trace_mode => Off => Off

mysqli

MysqlI Support => enabled
Client API library version => mysqlnd 5.0.10 - 20111026 - $Id: c85105d7c6f7d70d609bb4c000257868a40840ab $
Active Persistent Links => 0
Inactive Persistent Links => 0
Active Links => 0

Directive => Local Value => Master Value
mysqli.allow_local_infile => On => On
mysqli.allow_persistent => On => On
mysqli.default_host => no value => no value
mysqli.default_port => 3306 => 3306
mysqli.default_pw => no value => no value
mysqli.default_socket => /var/run/mysqld/mysqld.sock => /var/run/mysqld/mysqld.sock
mysqli.default_user => no value => no value
mysqli.max_links => Unlimited => Unlimited
mysqli.max_persistent => Unlimited => Unlimited
mysqli.reconnect => Off => Off

mysqlnd

mysqlnd => enabled
Version => mysqlnd 5.0.10 - 20111026 - $Id: c85105d7c6f7d70d609bb4c000257868a40840ab $
Compression => supported
SSL => supported
Command buffer size => 4096
Read buffer size => 32768
Read timeout => 31536000
Collecting statistics => Yes
Collecting memory statistics => No
Tracing => n/a
Loaded plugins => mysqlnd,example,debug_trace,auth_plugin_mysql_native_password,auth_plugin_mysql_clear_password
API Extensions => pdo_mysql,mysqli,mysql

mysqlnd statistics =>  
bytes_sent => 0
bytes_received => 0
packets_sent => 0
packets_received => 0
protocol_overhead_in => 0
protocol_overhead_out => 0
bytes_received_ok_packet => 0
bytes_received_eof_packet => 0
bytes_received_rset_header_packet => 0
bytes_received_rset_field_meta_packet => 0
bytes_received_rset_row_packet => 0
bytes_received_prepare_response_packet => 0
bytes_received_change_user_packet => 0
packets_sent_command => 0
packets_received_ok => 0
packets_received_eof => 0
packets_received_rset_header => 0
packets_received_rset_field_meta => 0
packets_received_rset_row => 0
packets_received_prepare_response => 0
packets_received_change_user => 0
result_set_queries => 0
non_result_set_queries => 0
no_index_used => 0
bad_index_used => 0
slow_queries => 0
buffered_sets => 0
unbuffered_sets => 0
ps_buffered_sets => 0
ps_unbuffered_sets => 0
flushed_normal_sets => 0
flushed_ps_sets => 0
ps_prepared_never_executed => 0
ps_prepared_once_executed => 0
rows_fetched_from_server_normal => 0
rows_fetched_from_server_ps => 0
rows_buffered_from_client_normal => 0
rows_buffered_from_client_ps => 0
rows_fetched_from_client_normal_buffered => 0
rows_fetched_from_client_normal_unbuffered => 0
rows_fetched_from_client_ps_buffered => 0
rows_fetched_from_client_ps_unbuffered => 0
rows_fetched_from_client_ps_cursor => 0
rows_affected_normal => 0
rows_affected_ps => 0
rows_skipped_normal => 0
rows_skipped_ps => 0
copy_on_write_saved => 0
copy_on_write_performed => 0
command_buffer_too_small => 0
connect_success => 0
connect_failure => 0
connection_reused => 0
reconnect => 0
pconnect_success => 0
active_connections => 0
active_persistent_connections => 0
explicit_close => 0
implicit_close => 0
disconnect_close => 0
in_middle_of_command_close => 0
explicit_free_result => 0
implicit_free_result => 0
explicit_stmt_close => 0
implicit_stmt_close => 0
mem_emalloc_count => 0
mem_emalloc_amount => 0
mem_ecalloc_count => 0
mem_ecalloc_amount => 0
mem_erealloc_count => 0
mem_erealloc_amount => 0
mem_efree_count => 0
mem_efree_amount => 0
mem_malloc_count => 0
mem_malloc_amount => 0
mem_calloc_count => 0
mem_calloc_amount => 0
mem_realloc_count => 0
mem_realloc_amount => 0
mem_free_count => 0
mem_free_amount => 0
mem_estrndup_count => 0
mem_strndup_count => 0
mem_estndup_count => 0
mem_strdup_count => 0
proto_text_fetched_null => 0
proto_text_fetched_bit => 0
proto_text_fetched_tinyint => 0
proto_text_fetched_short => 0
proto_text_fetched_int24 => 0
proto_text_fetched_int => 0
proto_text_fetched_bigint => 0
proto_text_fetched_decimal => 0
proto_text_fetched_float => 0
proto_text_fetched_double => 0
proto_text_fetched_date => 0
proto_text_fetched_year => 0
proto_text_fetched_time => 0
proto_text_fetched_datetime => 0
proto_text_fetched_timestamp => 0
proto_text_fetched_string => 0
proto_text_fetched_blob => 0
proto_text_fetched_enum => 0
proto_text_fetched_set => 0
proto_text_fetched_geometry => 0
proto_text_fetched_other => 0
proto_binary_fetched_null => 0
proto_binary_fetched_bit => 0
proto_binary_fetched_tinyint => 0
proto_binary_fetched_short => 0
proto_binary_fetched_int24 => 0
proto_binary_fetched_int => 0
proto_binary_fetched_bigint => 0
proto_binary_fetched_decimal => 0
proto_binary_fetched_float => 0
proto_binary_fetched_double => 0
proto_binary_fetched_date => 0
proto_binary_fetched_year => 0
proto_binary_fetched_time => 0
proto_binary_fetched_datetime => 0
proto_binary_fetched_timestamp => 0
proto_binary_fetched_string => 0
proto_binary_fetched_blob => 0
proto_binary_fetched_enum => 0
proto_binary_fetched_set => 0
proto_binary_fetched_geometry => 0
proto_binary_fetched_other => 0
init_command_executed_count => 0
init_command_failed_count => 0
com_quit => 0
com_init_db => 0
com_query => 0
com_field_list => 0
com_create_db => 0
com_drop_db => 0
com_refresh => 0
com_shutdown => 0
com_statistics => 0
com_process_info => 0
com_connect => 0
com_process_kill => 0
com_debug => 0
com_ping => 0
com_time => 0
com_delayed_insert => 0
com_change_user => 0
com_binlog_dump => 0
com_table_dump => 0
com_connect_out => 0
com_register_slave => 0
com_stmt_prepare => 0
com_stmt_execute => 0
com_stmt_send_long_data => 0
com_stmt_close => 0
com_stmt_reset => 0
com_stmt_set_option => 0
com_stmt_fetch => 0
com_deamon => 0
bytes_received_real_data_normal => 0
bytes_received_real_data_ps => 0

example statistics =>  
stat1 => 0
stat2 => 0

openssl

OpenSSL support => enabled
OpenSSL Library Version => OpenSSL 0.9.8o 01 Jun 2010
OpenSSL Header Version => OpenSSL 0.9.8o 01 Jun 2010

pcre

PCRE (Perl Compatible Regular Expressions) Support => enabled
PCRE Library Version => 8.32 2012-11-30

Directive => Local Value => Master Value
pcre.backtrack_limit => 1000000 => 1000000
pcre.recursion_limit => 100000 => 100000

PDO

PDO support => enabled
PDO drivers => mysql, odbc, sqlite

pdo_mysql

PDO Driver for MySQL => enabled
Client API version => mysqlnd 5.0.10 - 20111026 - $Id: c85105d7c6f7d70d609bb4c000257868a40840ab $

Directive => Local Value => Master Value
pdo_mysql.default_socket => /var/run/mysqld/mysqld.sock => /var/run/mysqld/mysqld.sock

PDO_ODBC

PDO Driver for ODBC (unixODBC) => enabled
ODBC Connection Pooling => Enabled, strict matching

pdo_sqlite

PDO Driver for SQLite 3.x => enabled
SQLite Library => 3.7.7.1

Phar

Phar: PHP Archive support => enabled
Phar EXT version => 2.0.1
Phar API version => 1.1.1
SVN revision => $Id: ec823514107160b7e6fabc519594012657a2db91 $
Phar-based phar archives => enabled
Tar-based phar archives => enabled
ZIP-based phar archives => enabled
gzip compression => enabled
bzip2 compression => enabled
Native OpenSSL support => enabled

Phar based on pear/PHP_Archive, original concept by Davey Shafik.
Phar fully realized by Gregory Beaver and Marcus Boerger.
Portions of tar implementation Copyright (c) 2003-2009 Tim Kientzle.
Directive => Local Value => Master Value
phar.cache_list => no value => no value
phar.readonly => On => On
phar.require_hash => On => On

posix

Revision => $Id: 1dfa9997ed76804e53c91e0ce862f3707617b6ed $

Reflection

Reflection => enabled
Version => $Id: f6367cdb4e3f392af4a6d441a6641de87c2e50c4 $

session

Session Support => enabled
Registered save handlers => files user 
Registered serializer handlers => php php_binary 

Directive => Local Value => Master Value
session.auto_start => Off => Off
session.cache_expire => 180 => 180
session.cache_limiter => nocache => nocache
session.cookie_domain => no value => no value
session.cookie_httponly => Off => Off
session.cookie_lifetime => 0 => 0
session.cookie_path => / => /
session.cookie_secure => Off => Off
session.entropy_file => /dev/urandom => /dev/urandom
session.entropy_length => 32 => 32
session.gc_divisor => 100 => 100
session.gc_maxlifetime => 1440 => 1440
session.gc_probability => 1 => 1
session.hash_bits_per_character => 4 => 4
session.hash_function => 0 => 0
session.name => PHPSESSID => PHPSESSID
session.referer_check => no value => no value
session.save_handler => files => files
session.save_path => no value => no value
session.serialize_handler => php => php
session.upload_progress.cleanup => On => On
session.upload_progress.enabled => On => On
session.upload_progress.freq => 1% => 1%
session.upload_progress.min_freq => 1 => 1
session.upload_progress.name => PHP_SESSION_UPLOAD_PROGRESS => PHP_SESSION_UPLOAD_PROGRESS
session.upload_progress.prefix => upload_progress_ => upload_progress_
session.use_cookies => On => On
session.use_only_cookies => On => On
session.use_trans_sid => 0 => 0

SimpleXML

Simplexml support => enabled
Revision => $Id: b9966ddccead3e8bb7666aae9de01fe3d687b21a $
Schema support => enabled

soap

Soap Client => enabled
Soap Server => enabled

Directive => Local Value => Master Value
soap.wsdl_cache => 1 => 1
soap.wsdl_cache_dir => /tmp => /tmp
soap.wsdl_cache_enabled => 1 => 1
soap.wsdl_cache_limit => 5 => 5
soap.wsdl_cache_ttl => 86400 => 86400

SPL

SPL support => enabled
Interfaces => Countable, OuterIterator, RecursiveIterator, SeekableIterator, SplObserver, SplSubject
Classes => AppendIterator, ArrayIterator, ArrayObject, BadFunctionCallException, BadMethodCallException, CachingIterator, CallbackFilterIterator, DirectoryIterator, DomainException, EmptyIterator, FilesystemIterator, FilterIterator, GlobIterator, InfiniteIterator, InvalidArgumentException, IteratorIterator, LengthException, LimitIterator, LogicException, MultipleIterator, NoRewindIterator, OutOfBoundsException, OutOfRangeException, OverflowException, ParentIterator, RangeException, RecursiveArrayIterator, RecursiveCachingIterator, RecursiveCallbackFilterIterator, RecursiveDirectoryIterator, RecursiveFilterIterator, RecursiveIteratorIterator, RecursiveRegexIterator, RecursiveTreeIterator, RegexIterator, RuntimeException, SplDoublyLinkedList, SplFileInfo, SplFileObject, SplFixedArray, SplHeap, SplMinHeap, SplMaxHeap, SplObjectStorage, SplPriorityQueue, SplQueue, SplStack, SplTempFileObject, UnderflowException, UnexpectedValueException

sqlite3

SQLite3 support => enabled
SQLite3 module version => 0.7
SQLite Library => 3.7.7.1

Directive => Local Value => Master Value
sqlite3.extension_dir => no value => no value

standard

Dynamic Library Support => enabled
Path to sendmail => /usr/sbin/sendmail -t -i 

Directive => Local Value => Master Value
assert.active => 1 => 1
assert.bail => 0 => 0
assert.callback => no value => no value
assert.quiet_eval => 0 => 0
assert.warning => 1 => 1
auto_detect_line_endings => 0 => 0
default_socket_timeout => 60 => 60
from => no value => no value
url_rewriter.tags => a=href,area=href,frame=src,form=,fieldset= => a=href,area=href,frame=src,form=,fieldset=
user_agent => no value => no value

tokenizer

Tokenizer Support => enabled

xml

XML Support => active
XML Namespace Support => active
libxml2 Version => 2.7.8

xmlreader

XMLReader => enabled

xmlrpc

core library version => xmlrpc-epi v. 0.51
php extension version => 0.51
author => Dan Libby
homepage => http://xmlrpc-epi.sourceforge.net
open sourced by => Epinions.com

xmlwriter

XMLWriter => enabled

xsl

XSL => enabled
libxslt Version => 1.1.26
libxslt compiled against libxml Version => 2.7.8
EXSLT => enabled
libexslt Version => 1.1.26

zip

Zip => enabled
Extension Version => $Id: abc21c7f1559e732dba6db94c69ecf638ae5fa3f $
Zip version => 1.11.0
Libzip version => 0.10.1

zlib

ZLib Support => enabled
Stream Wrapper => compress.zlib://
Stream Filter => zlib.inflate, zlib.deflate
Compiled Version => 1.2.3.4
Linked Version => 1.2.3.4

Directive => Local Value => Master Value
zlib.output_compression => Off => Off
zlib.output_compression_level => -1 => -1
zlib.output_handler => no value => no value

Additional Modules

Module Name
ionCube Loader

Environment

Variable => Value
LC_PAPER => de_DE.utf8
LC_MONETARY => de_DE.utf8
TERM => xterm
SHELL => /bin/bash
LC_NUMERIC => de_DE.utf8
OLDPWD => /var/www/web1/html/subdomains/playground_62/TYPO3.CMS
SSH_TTY => /dev/pts/1
USER => web1
MAIL => /var/mail/web1
PATH => /usr/local/bin:/usr/bin:/bin:/usr/games
PWD => /var/www/web1/html/subdomains/playground_62
LANG => de_DE.UTF-8
LC_MEASUREMENT => de_DE.utf8
SHLVL => 1
HOME => /var/www/web1
LOGNAME => web1
LC_CTYPE => de_DE.utf8
LC_TIME => de_DE.utf8
_ => /usr/local/bin/php54/php

PHP Variables

Variable => Value
_SERVER["LC_PAPER"] => de_DE.utf8
_SERVER["LC_MONETARY"] => de_DE.utf8
_SERVER["TERM"] => xterm
_SERVER["SHELL"] => /bin/bash
_SERVER["LC_NUMERIC"] => de_DE.utf8
_SERVER["OLDPWD"] => /var/www/web1/html/subdomains/playground_62/TYPO3.CMS
_SERVER["SSH_TTY"] => /dev/pts/1
_SERVER["USER"] => web1
_SERVER["MAIL"] => /var/mail/web1
_SERVER["PATH"] => /usr/local/bin:/usr/bin:/bin:/usr/games
_SERVER["PWD"] => /var/www/web1/html/subdomains/playground_62
_SERVER["LANG"] => de_DE.UTF-8
_SERVER["LC_MEASUREMENT"] => de_DE.utf8
_SERVER["SHLVL"] => 1
_SERVER["HOME"] => /var/www/web1
_SERVER["LOGNAME"] => web1
_SERVER["SSH_CONNECTION"] => XX.1XX.XX.XX 43191 XX.XX9.1XX.1XX 22
_SERVER["LC_CTYPE"] => de_DE.utf8
_SERVER["LC_TIME"] => de_DE.utf8
_SERVER["_"] => /usr/local/bin/php54/php
_SERVER["PHP_SELF"] => 
_SERVER["SCRIPT_NAME"] => 
_SERVER["SCRIPT_FILENAME"] => 
_SERVER["PATH_TRANSLATED"] => 
_SERVER["DOCUMENT_ROOT"] => 
_SERVER["REQUEST_TIME_FLOAT"] => 1392912171.7427
_SERVER["REQUEST_TIME"] => 1392912171
_SERVER["argv"] => Array
(
)

_SERVER["argc"] => 0
_ENV["LC_PAPER"] => de_DE.utf8
_ENV["LC_MONETARY"] => de_DE.utf8
_ENV["TERM"] => xterm
_ENV["SHELL"] => /bin/bash
_ENV["SSH_CLIENT"] => XX.XXX.XX.XX 43191 22
_ENV["LC_NUMERIC"] => de_DE.utf8
_ENV["OLDPWD"] => /var/www/web1/html/subdomains/playground_62/TYPO3.CMS
_ENV["SSH_TTY"] => /dev/pts/1
_ENV["USER"] => web1
_ENV["MAIL"] => /var/mail/web1
_ENV["PATH"] => /usr/local/bin:/usr/bin:/bin:/usr/games
_ENV["PWD"] => /var/www/web1/html/subdomains/playground_62
_ENV["LANG"] => de_DE.UTF-8
_ENV["LC_MEASUREMENT"] => de_DE.utf8
_ENV["SHLVL"] => 1
_ENV["HOME"] => /var/www/web1
_ENV["LOGNAME"] => web1
_ENV["SSH_CONNECTION"] => 89.183.XX.XX 43191 XX.1XX.1XX.1XX 22
_ENV["LC_CTYPE"] => de_DE.utf8
_ENV["LC_TIME"] => de_DE.utf8
_ENV["_"] => /usr/local/bin/php54/php

PHP License
This program is free software; you can redistribute it and/or modify
it under the terms of the PHP License as published by the PHP Group
and included in the distribution in the file:  LICENSE

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

If you did not receive a copy of the PHP license, or have any
questions about PHP licensing, please contact license@php.net.

Is this issue still valid or is it gone in latest master?

Unfortunately yes.

Running on commit d837f182f0d446b0f3b7b13f13b899cd71933285

/usr/local/bin/php55/php ~/html/subdomains/playground_62/TYPO3.CMS/typo3/cli_dispatch.phpsh 

Fatal error: Uncaught exception 'TYPO3\CMS\Core\Package\Exception\PackageStatesUnavailableException' with message 'The PackageStates.php file is either corrupt or unavailable.' in /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/core/Classes/Package/PackageManager.php:270
Stack trace:
#0 /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/core/Classes/Package/PackageManager.php(130): TYPO3\CMS\Core\Package\PackageManager->loadPackageStates()
#1 /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/core/Classes/Core/Bootstrap.php(319): TYPO3\CMS\Core\Package\PackageManager->initialize(Object(TYPO3\CMS\Core\Core\Bootstrap))
#2 /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/core/Classes/Core/Bootstrap.php(233): TYPO3\CMS\Core\Core\Bootstrap->initializePackageManagement('TYPO3\CMS\Core\...')
#3 /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/cli_dispatch.phpsh(48): TYPO3\CMS\Core\Core\Bootstrap->loadConfigurationAndInitialize()
#4 {main}
  thrown in /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/core/Classes/Package/PackageManager.php on line 270

I just deleted the packagesStates.php and truncated the typo3temp folder, for testing purposes.

within PackagesStates.php there´s mentioned that this file will be rewritten if not existant.

This does also not happen after doing the above tasks and recalling

/usr/local/bin/php55/php ./typo3/cli_dispatch.phpsh extbase 

Fatal error: Uncaught exception 'TYPO3\CMS\Core\Package\Exception\PackageStatesUnavailableException' with message 'The PackageStates.php file is either corrupt or unavailable.' in /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/core/Classes/Package/PackageManager.php:270
Stack trace:
#0 /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/core/Classes/Package/PackageManager.php(130): TYPO3\CMS\Core\Package\PackageManager->loadPackageStates()
#1 /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/core/Classes/Core/Bootstrap.php(319): TYPO3\CMS\Core\Package\PackageManager->initialize(Object(TYPO3\CMS\Core\Core\Bootstrap))
#2 /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/core/Classes/Core/Bootstrap.php(233): TYPO3\CMS\Core\Core\Bootstrap->initializePackageManagement('TYPO3\CMS\Core\...')
#3 /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/cli_dispatch.phpsh(48): TYPO3\CMS\Core\Core\Bootstrap->loadConfigurationAndInitialize()
#4 {main}
  thrown in /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/core/Classes/Package/PackageManager.php on line 270

After deletion of PackageStates.php a backend login was not passible. I was forced to open the installtool.

After running a regular compare a new PackageStates.php was present and I was able to talk to the extbase CLI but faced a new issue

 /usr/local/bin/php55/php ./typo3/cli_dispatch.phpsh extbase extension:install foo

Fatal error: Call to a member function preparseQuery() on a non-object in /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/extbase/Classes/Persistence/Generic/Storage/Typo3DbBackend.php on line 484

I can confirm the described behaviour of d.ros.
At the moment I don't have a working scheduler (it gives the same error as described). (beta7 and master)
The error

Fatal error: Call to a member function preparseQuery() on a non-object in /var/www/web1/html/subdomains/playground_62/TYPO3.CMS/typo3/sysext/extbase/Classes/Persistence/Generic/Storage/Typo3DbBackend.php on line 484

only occurred after checking out master, and not updating the database. After a database compare (adding the extbase_queries table), the error was gone. (but stuck again with the original error message).
I did remove PackageStates as well, and it didn't fix the problem, so I assume the problem is somewhere else (as others reported they could not reproduce the problem with the exact same PackageStates file).

I have a similar issue:

Call to a member function preparseQuery() on a non-object in /usr/share/typo3/typo3_src-6.2.0rc1/typo3/sysext/extbase/Classes/Persistence/Generic/Storage/Typo3DbBackend.php on line 484, referer: http://afiliatys.tidi.be/typo3/backend.php

The error occurs at several locations:

• The page where a femanager and femanagerextended is loading
• Powermail backend module
• The language backend module
• The extension manager
• Backend users
• Log

I tried to remove the femanager* extensions, but nu effect.
I tried a compare database and updated, but the only effect is a can't rollback

After removing the APC caching, disabled module + removed config caching. I was able to so the most again. i also was able to install the femanager* extensions again.

APC Configuration

APC Support => disabled
Version => 3.1.13
APC Debugging => Disabled
MMAP Support => Enabled
MMAP File Mask =>  
Locking type => pthread mutex Locks
Serialization Support => broken
Revision => $Revision: 327136 $
Build Date => Sep  4 2012 20:01:41

Directive => Local Value => Master Value
apc.cache_by_default => On => On
apc.canonicalize => On => On
apc.coredump_unmap => Off => Off
apc.enable_cli => Off => Off
apc.enabled => On => On
apc.file_md5 => Off => Off
apc.file_update_protection => 2 => 2
apc.filters => no value => no value
apc.gc_ttl => 3600 => 3600
apc.include_once_override => Off => Off
apc.lazy_classes => Off => Off
apc.lazy_functions => Off => Off
apc.max_file_size => 5M => 5M
apc.mmap_file_mask => no value => no value
apc.num_files_hint => 10000 => 10000
apc.preload_path => no value => no value
apc.report_autofilter => Off => Off
apc.rfc1867 => Off => Off
apc.rfc1867_freq => 0 => 0
apc.rfc1867_name => APC_UPLOAD_PROGRESS => APC_UPLOAD_PROGRESS
apc.rfc1867_prefix => upload_ => upload_
apc.rfc1867_ttl => 3600 => 3600
apc.serializer => default => default
apc.shm_segments => 1 => 1
apc.shm_size => 512M => 512M
apc.shm_strings_buffer => 4M => 4M
apc.slam_defense => Off => Off
apc.stat => On => On
apc.stat_ctime => Off => Off
apc.ttl => 0 => 0
apc.use_request_time => On => On
apc.user_entries_hint => 4096 => 4096
apc.user_ttl => 0 => 0
apc.write_lock => On => On

I can confirm this error. After updating from typo3 6.2 beta7 to 6.2rc2.

 Call to a member function preparseQuery() on a non-object in /typo3_src-6.2.0rc2/typo3/sysext/extbase/Classes/Persistence/Generic/Storage/Typo3DbBackend.php on line 483

this error appears from the extensionmanager and the frontend

As I understand the preparseQuery is another issue ... please truncate all database tables which starts with "cf_" and report back if this solves that issue.

What I forgot: it happens by updating from beta7 to any RC*

@Alexander: Since I've solved the problem by deleting all kinds of cache, I can not reproduce the error and try your fix.

In case it helps anyone:

A developer here ran into this today, and we found that it depends on if we use the "typo3" symlink or not when calling the dispatcher. When called like this, it works fine:

typo3/cli_dispatch.phpsh

When called the following way, we get the "PackageStates" error (and the system seems to get the folder context wrong -- it writes a "typo3_src/typo3temp" folder):

typo3_src/typo3/cli_dispatch.phpsh

Gabe Blair wrote:

In case it helps anyone:

A developer here ran into this today, and we found that it depends on if we use the "typo3" symlink or not when calling the dispatcher. When called like this, it works fine:

[...]

When called the following way, we get the "PackageStates" error (and the system seems to get the folder context wrong -- it writes a "typo3_src/typo3temp" folder):

[...]

I can confirm that this seems to be the issue.