make: fix #1197

Partial revert of 85b7eca19edf76a5b82c2ebe01e0e90a3292dee7

Fixes #1197.
documentation: clean up doxygen mess after cortex

fixes #1190
Merge pull request #1194 from LudwigOrtmann/cortexygen

documentation: fix generation Doxygen documentation after Cortex import
Merge pull request #1198 from Kijewski/issue-1197

make: fix rebuilding on changes without `clean` or `-B`
tests: added a thread_sleep() at the end

Letting the main thread exit could cause failing test if thread_exit()
is broken for the tested platform, preventing the actual testing of the
hwtimer.
Merge pull request #1083 from OlegHahm/test_hwtimer_w_thread_sleep

tests: added a thread_sleep() at the end
Refactored crypto module into structured directoy layout

* crypto ciphers now located in sys/crypto/chipers/*
* crypto hashes now located in sys/crypto/hashes/*
Added cipher mode operation support

The following cipher modes are now supported
* Electronic code book (ECB)
* Cipher block chaining (CBC)
* Counter (CTR)
* Counter with CBC-MAC (CCM)
Added tests for aes and aes with ccm mode
Fix strict-prototypes errors
crypto/modes/helper.h: Move comparison into while condition
Fix ccn-lite-client and ccn-lite-relay
Fixed typos and parameter ordering for several crypto ciphers
Added crypto shell - basic encryption/decryption for supported ciphers