Custom libaries are gone FYI

Despite some assurances that upgrading IDE WILL NOT affect custom libraries my new 1.6.6 lost links to several of them.

And same time it claims that some of them are invalid.

An example - cannot find variant. h

No big issue , I saved my old 1.6.5.

This is just FYI.

PS I had to cut most of the error messages so it will fit, so only some of them are somewhat descriptive of this issue.

Arduino: 1.6.6 Hourly Build 2015/06/30 04:02 (Windows XP), Board: "Arduino Due (Programming Port)"

\Temp\build1177757462091613439.tmp\libraries\LiquidCrystal\LiquidCrystal.cpp.o 
In file included from C:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\hardware\sam\1.6.4\cores\arduino/Stream.h:26:0,
                 from C:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\hardware\sam\1.6.4\cores\arduino/HardwareSerial.h:24,
                 from C:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\hardware\sam\1.6.4\cores\arduino/Arduino.h:183,
                 from C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\LiquidCrystal\LiquidCrystal.cpp:36:
C:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\hardware\sam\1.6.4\cores\arduino/Print.h:23:46: note: #pragma message: Including modified print.h
 #pragma message ("Including modified print.h") 
                                              ^
C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\LiquidCrystal\LiquidCrystal.cpp:41:40: note: #pragma message: Using LiquidCrystal.h
 #pragma message("Using LiquidCrystal.h")
                                        ^
C:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\tools\arm-none-eabi-gcc\4.8.3-2014q1/bin/arm-none-eabi-g++ -c -g -Os -w -ffunction-sections -fdata-sections -nostdlib -fno-threadsafe-statics --param max-inline-insns-single=500 -fno-rtti -fno-exceptions -Dprintf=iprintf -MMD -mcpu=cortex-m3 -DF_CPU=84000000L -DARDUINO=10606 -DARDUINO_SAM_DUE -DARDUINO_ARCH_SAM -D__SAM3X8E__ -mthumb -DUSB_VID=0x2341 -DUSB_PID=0x003e -DUSBCON -DUSB_MANUFACTURER="Unknown" -DUSB_PRODUCT="Arduino Due" -IC:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\hardware\sam\1.6.4\system/libsam -IC:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\hardware\sam\1.6.4\system/CMSIS/CMSIS/Include/ -IC:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\hardware\sam\1.6.4\system/CMSIS/Device/ATMEL/ -IC:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\hardware\sam\1.6.4\cores\arduino -IC:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\hardware\sam\1.6.4\variants\arduino_due_x -IC:\Documents and Settings\Vaclav\Local Settings\Application Data\Arduino15\packages\arduino\hardware\sam\1.6.4\libraries\Wire -IC:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\LiquidCrystal -IC:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\LiquidCrystal\utility C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\LiquidCrystal\LiquidCrystal_I2C.cpp -o C:\DOCUME~1\Vaclav\LOCALS~1\Temp\build1177757462091613439.tmp\libraries\LiquidCrystal\LiquidCrystal_I2C.cpp.o 
C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\LiquidCrystal\LiquidCrystal_I2C.cpp:40:119: fatal error: ..\..\..\..\Application Data\arduino15\packages\arduino\hardware\sam\1.6.4\variants\arduino_due_x\variant.h: No such file or directory
 #include "..\..\..\..\Application Data\arduino15\packages\arduino\hardware\sam\1.6.4\variants\arduino_due_x\variant.h"
                                                                                                                       ^
compilation terminated.
Error compiling.
Invalid library found in C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\FATS: C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\FATS
Invalid library found in C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\minmsc_2013_11_27_v1_1: C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\minmsc_2013_11_27_v1_1
Invalid library found in C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\USB_MSC_Minimal: C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\USB_MSC_Minimal
Invalid library found in C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\FATS: C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\FATS
Invalid library found in C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\minmsc_2013_11_27_v1_1: C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\minmsc_2013_11_27_v1_1
Invalid library found in C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\USB_MSC_Minimal: C:\Documents and Settings\Vaclav\My Documents\Arduino\libraries\USB_MSC_Minimal