Add doxygen configuration

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+Memory Addressing
+=================
+ There is 3 types of addresses: virtual, physical, and bus. For DMA a bus
+ address is used. However, on x86 physical and  bus addresses are the same (on
+ other architectures it is not guaranteed). Anyway, this assumption is still
+ used by xdma driver, it uses phiscal address for DMA access. I have ported
+ in the same way. Now, we need to provide additionaly bus-addresses in kmem
+ abstraction and use it in NWL DMA implementation.
+
+DMA Access Synchronization
+==========================
+ - At driver level, few types of buffers are supported:
+    * SIMPLE - non-reusable buffers, the use infomation can be used for cleanup
+    after crashed applications.
+    * EXCLUSIVE - reusable buffers which can be mmaped by a single appliction
+    only. There is two modes of these buffers:
+	+ Buffers in a STANDARD mode are created for a single DMA operation and
+	if such buffer is detected while trying to reuse, the last operation
+	has failed and reset is needed.
+	+ Buffers in a PERSISTENT mode are preserved between invocations of
+	control application and cleaned up only after the PERSISTENT flag is 
+	removed
+    * SHARED - reusable buffers shared by multiple processes. Not really 
+    needed at the moment.
+
+    KMEM_FLAG_HW - indicates that buffer can be used by hardware, acually this
+    means that DMA will be enabled afterwards. The driver is not able to check
+    if it really was enable and therefore will block any attempt to release 
+    buffer until KMEM_HW_FLAG is passed to kmem_free routine as well. The later
+    should only called with KMEM_HW_FLAG after the DMA engine is stopped. Then,
+    the driver can be realesd by kmem_free if ref count reaches 0.
+    
+    KMEM_FLAG_EXCLUSIVE - prevents multiple processes mmaping the buffer 
+    simultaneously. This is used to prevent multiple processes use the same
+    DMA engine at the same time. When passed to kmem_free, allows to clean
+    buffers with lost clients even for shared buffers.
+    
+    KMEM_FLAG_REUSE - requires reuse of existing buffer. If reusable buffer is 
+    found (non-reusable buffers, i.e. allocated without KMEM_FLAG_REUSE are
+    ignored), it is returned instead of allocation. Three types of usage 
+    counters are used. At moment of allocation, the HW reference is set if 
+    neccessary. The usage counter is increased by kmem_alloc function and
+    decreased by kmem_free. Finally, the reference is obtained at returned
+    during mmap/munmap. So, on kmem_free, we do not clean
+	a) buffers with reference count above zero or hardware reference set.
+	REUSE flag should be supplied, overwise the error is returned
+	b) PERSISTENT buffer. REUSE flash should be supplied, overwise the 
+	error is returned
+	c) non-exclusive buffers with usage counter above zero (For exclusive
+	buffer the value of usage counter above zero just means that application
+        have failed without cleaning buffers first. There is no easy way to 
+        detect that for shared buffers, so it is left as manual operation in
+        this case)
+        d) any buffer if KMEM_FLAG_REUSE was provided to function
+    During module unload, only buffers with references can prevent cleanup. In
+    this case the only possiblity to free the driver is to call kmem_free 
+    passing FORCE flags.
+    
+    KMEM_FLAG_PERSISTENT - if passed to allocation routine, changes mode of 
+    buffer to PERSISTENT, if passed to free routine, vice-versa changes mode
+    of buffer to NORMAL. Basically, if we call 'pci --dma-start' this flag
+    should be passed to alloc and if we call 'pci --dma-stop' it should be
+    passed to free. In other case, the flag should not be present.
+
+    If application crashed, the munmap while be still called cleaning software
+    references. However, the hardware reference will stay since it is not clear
+    if hardware channel was closed or not. To lift hardware reference, the 
+    application can be re-executed (or dma_stop called, for instance).
+    * If there is no hardware reference, the buffers will be reused by next 
+    call to application and for EXCLUSIVE buffer cleaned at the end. For SHARED
+    buffers they will be cleaned during module cleanup only (no active 
+    references).
+    * The buffer will be reused by next call which can result in wrong behaviour
+    if buffer left in incoherent stage. This should be handled on upper level.
+    
+ - At pcilib/kmem level synchronization of multiple buffers is performed
+    * The HW reference and following modes should be consistent between member 
+    parts: REUSABLE, PERSISTENT, EXCLUSIVE (only HW reference and PERSISTENT 
+    mode should be checked, others are handled on dirver level)
+    * It is fine if only part of buffers are reused and others are newly 
+    allocated. However, on higher level this can be checked and resulting
+    in failure.
+    
+    Treatment of inconsistencies:
+     * Buffers are in PRESISTENT mode, but newly allocated, OK
+     * Buffers are reused, but are not in PERSISTENT mode (for EXCLUSIVE buffers
+     this means that application has crashed during the last execution), OK
+     * Some of buffers are reused (not just REUSABLE, but actually reused), 
+     others - not, OK until 
+        a) either PERSISTENT flag is set or reused buffers are non-PERSISTENT
+	b) either HW flag is set or reused buffers does not hold HW reference
+     * PERSISTENT mode inconsistency, FAIL (even if we are going to set 
+     PERSISTENT mode anyway)
+     * HW reference inconsistency, FAIL (even if we are going to set 
+     HW flag anyway)
+     
+    On allocation error at some of the buffer, call clean routine and
+     * Preserve PERSISTENT mode and HW reference if buffers held them before
+     unsuccessful kmem initialization. Until the last failed block, the blocks
+     of kmem should be consistent. The HW/PERSISTENT flags should be removed
+     if all reused blocks were in HW/PERSISTENT mode. The last block needs
+     special treatment. The flags may be removed for the block if it was
+     HW/PERSISTENT state (and others not).
+     * Remove REUSE flag, we want to clean if allowed by current buffer status
+     * EXCLUSIVE flag is not important for kmem_free routine.
+    
+ - At DMA level
+    There is 4 components of DMA access:
+    * DMA engine enabled/disabled
+    * DMA engine IRQs enabled/disabled - always enabled at startup
+    * Memory buffers
+    * Ring start/stop pointers
+    
+    To prevent multiple processes accessing DMA engine in parallel, the first
+    action is buffer initialization which will fail if buffers already used
+	* Always with REUSE, EXCLUSIVE, and HW flags 
+	* Optionally with PERSISTENT flag (if DMA_PERSISTENT flag is set)
+    If another DMA app is running, the buffer allocation will fail (no dma_stop 
+    is executed in this case) 
+
+    Depending on PRESERVE flag, kmem_free will be called with REUSE flag 
+    keeping buffer in memory (this is redundant since HW flag is enough) or HW
+    flag indicating that DMA engine is stopped and buffer could be cleaned.
+    PERSISTENT flag is defined by DMA_PERSISTENT flag passed to stop routine.
+    
+    PRESERVE flag is enforced if DMA_PERSISTENT is not passed to dma_stop
+    routine and either it:
+	a) Explicitely set by DMA_PERMANENT flag passed to dma_start 
+	function 
+	b) Implicitely set if DMA engine is already enabled during dma_start, 
+	all buffers are reused, and are in persistent mode.
+    If PRESERVE flag is on, the engine will not be stopped at the end of
+    execution (and buffers will stay because of HW flag).
+    
+    If buffers are reused and are already in PERSISTENT mode, DMA engine was on 
+    before dma_start (PRESERVE flag is ignored, because it can be enforced), 
+    ring pointers are calculated from LAST_BD and states of ring elements.
+    If previous application crashed (i.e. buffers may be corrupted). Two
+    cases are possible:
+    * If during the call buffers were in non-PERSISTENT mode, it can be 
+    easily detected - buffers are reused, but are not in PERSISTENT mode 
+    (or at least was not before we set them to). In this case we just 
+    reinitialize all buffers.
+    * If during the call buffers were in PERSISTENT mode, it is up to 
+    user to check their consistency and restart DMA engine.]
+    
+    IRQs are enabled and disabled at each call
+
+DMA Reads
+=========
+standard: 		default reading mode, reads a single full packet
+multipacket:		reads all available packets
+waiting multipacket:	reads all available packets, after finishing the
+			last one waiting if new data arrives
+exact read:		read exactly specified number of bytes (should be
+			only supported if it is multiple of packets, otherwise
+			error should be returned)
+ignore packets:		autoterminate each buffer, depends on engine 
+			configuration
+
+ To handle differnt cases, the value returned by callback function instructs
+the DMA library how long to wait for the next data to appear before timing 
+out. The following variants are possible:
+terminate:		just bail out
+check:			no timeout, just check if there is data, otherwise 
+			terminate
+timeout:		standard DMA timeout, normaly used while receiving
+			fragments of packet: in this case it is expected 
+			that device has already prepared data and only
+			the performance of DMA engine limits transfer speed
+wait:			wait until the data is prepared by the device, this
+			timeout is specified as argument to the dma_stream
+			function (standard DMA timeout is used by default)
+
+			first |  new_pkt  | bufer 
+			--------------------------	
+standard		wait  | term      | timeout  
+multiple packets	wait  | check	  | timeout 	- DMA_READ_FLAG_MULTIPACKET 	
+waiting multipacket	wait  | wait      | timeout 	- DMA_READ_FLAG_WAIT
+exact			wait  | wait/term | timeout	- limited by size parameter
+ignore packets		wait  | wait/check| wait/check 	- just autoterminated
+
+Shall we do a special handling in case of overflow?
+    
+
+Buffering
+=========
+ The DMA addresses are limited to 32 bits (~4GB for everything). This means we 
+ can't really use DMA pages are sole buffers. Therefore, a second thread, with
+ a realtime scheduling policy if possible, will be spawned and will copy the 
+ data from the DMA pages into the allocated buffers. On expiration of duration
+ or number of events set by autostop call, this thread will be stopped but 
+ processing in streaming mode will continue until all copyied data is passed 
+ to the callbacks.
+
+ To avoid stalls, the IPECamera requires data to be read continuously read out.
+ For this reason, there is no locks in the readout thread. It will simplify
+ overwrite the old frames if data is not copied out timely. To handle this case
+ after getting the data and processing it, the calling application should use
+ return_data function and check return code. This function may return error
+ indicating that the data was overwritten meanwhile. Hence, the data is 
+ corrupted and shoud be droped by the application. The copy_data function
+ performs this check and user application can be sure it get coherent data
+ in this case.
+ 
+ There is a way to avoid this problem. For raw data, the rawdata callback
+ can be requested. This callback blocks execution of readout thread and 
+ data may be treated safely by calling application. However, this may 
+ cause problems to electronics. Therefore, only memcpy should be performed
+ on the data normally. 
+
+ The reconstructed data, however, may be safely accessed. As described above,
+ the raw data will be continuously overwritten by the reader thread. However,
+ reconstructed data, upon the get_data call, will be protected by the mutex.
+
+
+Register Access Synchronization
+===============================
+ We need to serialize access to the registers by the different running 
+ applications and handle case when registers are accessed indirectly by
+ writting PCI BARs (DMA implementations, for instance).
+
+ - Module-assisted locking:
+ * During initialization the locking context is created (which is basicaly
+ a kmem_handle of type LOCK_PAGE. 
+ * This locking context is passed to the kernel module along with lock type 
+ (LOCK_BANK) and lock item (BANK ADDRESS). If lock context is already owns
+ lock on the specified bank, just reference number is increased, otherwise
+ we are trying to obtain new lock.
+ * Kernel module just iterates over all registered lock pages and checks if
+ any holds the specified lock. if not, the lock is obtained and registered
+ in the our lock page.
+ * This allows to share access between multiple threads of single application
+ (by using the same lock page) or protect (by using own lock pages by each of
+ the threads)
+ * Either on application cleanup or if application crashed, the memory mapping
+ of lock page is removed and, hence, locks are freed.
+ 
+ - Multiple-ways of accessing registers
+ Because of reference counting, we can successfully obtain locks multiple 
+ times if necessary. The following locks are protecting register access:
+  a) Global register_read/write lock bank before executing implementation
+  b) DMA bank is locked by global DMA functions. So we can access the 
+  registers using plain PCI bar read/write.
+  c) Sequence of register operations can be protected with pcilib_lock_bank
+  function
+ Reading raw register space or PCI bank is not locked.
+  * Ok. We can detect banks which will be affected by PCI read/write and 
+  lock them. But shall we do it?
+ 
+Register/DMA Configuration
+==========================
+ - XML description of registers
+ - Formal XML-based (or non XML-based) language for DMA implementation. 
+   a) Writting/Reading register values
+   b) Wait until <register1>=<value> on <register2>=<value> report error
+   c) ... ?
+
+IRQ Handling
+============
+ IRQ types: DMA IRQ, Event IRQ, other types
+ IRQ hardware source: To allow purely user-space implementation, as general
+ rule, only a  single (standard) source should be used.
+ IRQ source: The dma/event engines, however, may detail this hardware source
+ and produce real IRQ source basing on the values of registers. For example, 
+ for DMA IRQs the source may present engine number and for Event IRQs the 
+ source may present event type.
+
+ Only types can be enabled or disabled. The sources are enabled/disabled
+ by enabling/disabling correspondent DMA engines or Event types. The expected
+ workflow is following:
+ * We enabling IRQs in user-space (normally setting some registers). Normally,
+ just an Event IRQs, the DMA if necessary will be managed by DMA engine itself.
+ * We waiting for standard IRQ from hardware (driver)
+ * In the user space, we are checking registers to find out the real source
+ of IRQ (driver reports us just hardware source), generating appropriate 
+ events, and acknowledge IRQ. This is dependent on implementation and should 
+ be managed inside event API.
+ 
+ I.e. the driver implements just two methods pcilib_wait_irq(hw_source), 
+ pcilib_clear_irq(hw_source). Only a few hardware IRQ sources are defined.
+ In most cirstumances, the IRQ_SOURCE_DEFAULT is used. 
+ 
+ The DMA engine may provide 3 additional methods, to enable, disable,
+ and acknowledge IRQ.
+ 
+ ... To be decided in details upon the need...
+
+Updating Firmware
+=================
+ - JTag should be connected to USB connector on the board (next to Ethernet)
+ - The computer should be tourned off and on before programming
+ - The environment variable should be loaded
+    . /home/uros/.bashrc
+ - The application is called 'impact'
+    No project is needed, cancel initial proposals (No/Cancel)
+    Double-click on "Boundary Scan"
+    Right click in the right window and select "Init Chain"
+    We don't want to select bit file now (Yes and, then, click Cancel)
+    Right click on second (right) item and choose "Assign new CF file"
+    Select a bit file. Answer No, we don't want to attach SPI to SPI Prom
+    Select xv6vlx240t and program it
+ - Shutdown and start computer
+ 
+ Firmware are in
+    v.2: /home/uros/Repo/UFO2_last_good_version_UFO2.bit
+    v.3: /home/uros/Repo/UFO3 
+	Step5 - best working revision
+	Step6 - last revision
+
+    
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