STM32F7 QSPI flash timeouts and 4-byte addressing (#152) ...

* STM32F7: Unconditionally enable QSPI workarounds

On the STM32769NI at least this patch is required for stable QSPI use.
Enable it uncondtionally in case other boards need it too.

Further discussions:

https://github.com/ARMmbed/mbed-os/issues/10049
https://github.com/ARMmbed/mbed-os/issues/15108

https://github.com/STMicroelectronics/STM32CubeF7/issues/52
https://github.com/STMicroelectronics/STM32CubeF7/issues/82

* QSPIF: Attempt 4-byte addressing on Macronix chips

mbed-os PR 11531 introduced 4-byte addressing in the QSPIF block device:

https://github.com/ARMmbed/mbed-os/pull/11531

During testing it was found that this code broke on the NRF52840_DK and
DISCO_F769NI.

The NRF52840_DK controller seems unable to handle 4-byte addressing at
all and has been disabled entirely in another code section.

The DISCO_F769NI breakage was attributed to the flash chip but after more
research I believe this is related to the QSPI controller, not the 4-byte
addressing itself.

Now that the QSPI controller has a workaround, enable 4-byte addressing
again and hope it works fine this time.

Fix all Doxygen errors and make any future errors fatal (#118) ...

* Start working on fixing doxygen warnings

* Upgrade doxyfile to Doxygen 1.9.1

* Clean up some unmatched groups and add some exclusions

* Fix docs for rtos::ThisThread not showing up

* Fix up KV store docs

* Fix incorrect @files, some more incorrect groups

* Fix lots of broken links

* Start fixing mbedtls groups

* Fix more mbedtls docs

* Fix remaining mbedtls files with missing or incorrect grouping

* Fix a huge amount of PSA docs errors

* Fix a few more mbedtls docs errors

* Fix __cplusplus not defined for docs, clean up call in callback typedef, fix some docs errors

* Fix some broken doc links in HAL headers

* Fix more PSA doc errors

* Fix some doxygen errors in networking code

* Fix lots of network related doc errors

* Try and fix some CI failures

* Use Doxygen Action instead of doxygen in Mbed container to get the right version

* Try removing docs check

* Add first part of doxygen action

* Add next part of doxygen action

* Fix yaml syntax error

* Add in license check fix

* Try using verbose scancode

* Fix some more docs issues, workaround scancode-toolkit#3179

* Clean up the LoRaRadio get_state() function on each implementation.  Also fix some other compile and doc errors.

* Fix all remaining doxygen errors

* Fix escaping, for realsies this time

* Remove Doxygen unsupported config options, fix some more get_status() declarations

* Fix some UNITTESTS build errors

* Fix one more compile error

* Another unittest error

Clean up group/module definitions in doxygen (#97) ...

* Clean up group definitions in doxygen

* remove THIRD_PARTY_DOCS

* some stragglers

* fix astyle formatting

Lots of usability improvements for the I2C API. Better docs and new top-level functions. (#64) ...

* Lots of usability improvements for the I2C API.  Better docs and new top-level functions.

* Document frequencies

* Tabs to spaces

* More style fixes

* Run astyle

* Clean up docs

* Add note about addressing, change 10 bit to 11 bit

* Fix spellcheck

* Fix paste error

* Oops, fix accidental change

Allow SDBlockDevice to use either HW or SW chip selects

Fix some build errors

Fix ABI differences between mbed-baremetal and mbed-os, remove PlatformMutex

Rename inconsistently named testing-related variables. Also fix STM32CUBE not working from application code.

Convert storage/ targets into STATIC libraries

Clean up top-level build file and build options, fix build issues on MinGW

Fix missing mbed:: profix issue

QSPIF: Add missing mbed namespace prefix to header file

CMake: QSPIFBlockDevice: Guard unit test directory ...

In the QSPIFBlockDevice component we checked if BUILD_TESTING was
enabled before adding the QSPIFBlockDevice/UNITTESTS subdirectory. In
the parent blockdevice/CMakeLists.txt we added the QSPIFBlockDevice
subdirectory to the build under two separate conditions:

* when "QSPIF" is present in MBED_TARGET_LABELS
* when building only unit tests

This wasn't quite enough, as when we build greentea tests for some
targets QSPIF is enabled in MBED_TARGET_LABELS, causing the
QSPIFBlockDevice subdirectory and its unit tests to be added when
building greentea tests. This caused a test failure on targets which
enable QSPIF:

```
The following tests FAILED:
	 40 - qspif-unittest_NOT_BUILT (Not Run)
```

To fix this we need to specifically check that we're not building
greentea tests before adding the QSPIFBlockDevice/UNITTESTS directory to
the project.

Part of this issue is our reliance on MBED_TARGET_LABELS to pull
features in to the build. We should refactor our usage of
MBED_TARGET_LABELS and use CMake target dependencies where possible.
Then we wouldn't need to add subdirectories under various, often
conflicting, scenarios. Instead the targets would always be available
and we would just choose which ones to actually build in different cases
using CMake target linking.

SFDP: Add support for multiple configurations and sector maps ...

A Sector Map Parameter Table contains a sequence of the following
descriptors:
* (Optional) configuration detection command descriptors, one for
each command to run to determine the current configuration. This
exists only if the flash layout is configurable.
* Sector map descriptors, one for each possible configuration. On
a flash device with a non-configurable layout, there is only one
such descriptor.

Previously we only supported the non-configurable case with a single
descriptor. This commit adds support for multiple configurations.

QSPIFBlockDevice: Add unit test for the S25FS512S quirk ...

Add a test case to verify that the quirk on `CR1NV` and `CR3NV`
registers get applied by `QSPIFBlockDevice` when the flash device
is S25FS512S.

`QSPIFBlockDevice` depends on the SFDP functions and the `QSPI` class,
but we can't use gMock on them because:
* SFDP functions are global functions, whereas gMock only supports
mocking class member functions.
* A mocked class is injected into the test subject, but passing a
preexisting `QSPI` instance into `QSPIFBlockDevice` is not possible
(unless we resort to pointers). For details, see comments in
test_QSPIFBlockDevice.cpp.

So fakes of the `QSPI` class and any SFDP functions involved are
defined in test_QSPIFBlockDevice.cpp.

QSPIFBlockDevice: Add quirk to ignore overlaying sectors on S25FS512S ...

The entire flash chip S25FS512S consists of uniform 256KB sectors.
Additionally, it has three configurations:
* 0x01: Eight 4KB sectors (32KB in total) overlaying the start of
the first 256KB sector
* 0x03: Eight 4KB sectors (32KB in total) overlaying the end of the
last 256KB sector
* 0x05: No overlaying sectors

The active configuration is determined from bit fields of two
registers, CR1NV and CR3NV.

Mbed OS does not currently support partially overlaying sectors,
meaning that with eight 4KB sectors overlay a 256KB sectors, the
remaining 224KB (== 256KB - 8 * 4KB) of the big sector can't be
correctly handled. Supporting such scenario would involve a large
amount of rewriting in Mbed OS's BlockDevice, SFDP and their tests,
and may increase the code size.

So, this commit applies a quirk to always report configuration 0x05
(no overlaying sectors). Even if 0x01 or 0x03 is the real configuration,
they are compatible with the 0x05 configuration because 256KB sectors
exist in all cases.

Note: This quirk does *not* change actual configurations on hardware,
because registers CR1NV and CR3NV are one-time configurable (OTP) -
each bit field has a factory value of 0 and can be changed to 1 by the
user but not back to 0. So QSPIFBlockDevice avoids changing them.

QSPIFBlockDevice: Add quirk for inconsistent CR3NV register value ...

Cypress S25FS512S's SFDP table suggests that bit-1 of the register
CR3NV on 25FS512S should equal 1. But it is a known issue that the
value is actually 0 on hardware. So if we query the value of CR3NV
during configuration detection, we can't find a configuration that
matches the SFDP data. This issue has been discussed in the Linux MTD
(Memory Technology Devices) mailing list:
https://linux-mtd.infradead.narkive.com/ylHK6CyT/spi-nor-fs512s-incorrect-cr3nv-1-value

This commit adds a quirk to report bit-1 of CR3NV as 1.

Note: In Mbed OS, vendor-specific quirks can only be handled in block
devices. The SFDP functions assume data from hardware to be correct.
So this quirk is in the block device.

QSPIFBlockDevice: Use fully-qualified include path ...

In Mbed OS, each library has an `include/<library>/` subdirectory
containing headers. The recommended way to include a header is
`#include "<library>/<header>.h"` to avoid potential conflicts with
any external modules that have same names of headers.

This is not enforced yet, and both include/ and include/<component>/
are in a library's include paths, to avoid breaking preexisting
Mbed projects that don't follow the recommendation. But code within
Mbed OS should follow it at least.

SFDP: unit tests: Fix Configuration ID in fake test data ...

The second byte of the sector map descriptor is the configuration ID.
On a device with non-configurable layout, the only available map
descriptor's configuration ID must be 0x00 as required by the
JESD216D standard. This value is important, because we will check
each descriptor's configuration ID when we support multiple
configurations.

Note: The test data is fake - when we modified real data of a
configurable device to become non-configurable for test purpose, we
forgot to change this field.

SFDP: unit tests: Move unshared test data into case ...

Some test data in test_sfdp.cpp is used by one test case only, so
we turn it into a local variable.

SFDP: Add more parameters to the reader callback ...

The SFDP functions parse SFDP data which is fetched by a callback
called `sfdp_reader` provided by {SPIF,QSPIF,OSPIF}BlockDevice.
Currently, this callback interface only takes a read address and an RX
buffer to store output data. This has been enough, because other SPI
parameters are always the same when fetching the SFDP table only -
they are just hardcoded in each reader.

But in the future we will add support for flash devices with multiple
configurations (in a subsequent commit), and to detect which
configuration is enabled, we will need to send detection commands
which require device-dependent SPI parameters:
* address size
* instruction
* dummy cycles

This commit
* turns the above SPI parameters from predefined/hardcoded values
into parameters of the callback
* lets the SFDP functions pass the above parameters to the callback
(Note: To read the SFDP table itself, those values are constants
defined by the standard, not tied to any particular device, so they
can be known to the SFDP functions)
* updates the callbacks implemented by {SPIF,QSPIF,OSPIF}BlockDevice
* updates the mock callback for unit tests and expectations

SFDP: Fix sector map table allocation check ...

When passing an allocation size directly to `std::make_unique`,
`std::nothrow` is unavailable, so any failed allocation results in
an exception which we cannot catch because Mbed OS is compiled with
`-fno-exceptions`. To fix this, chain `std::make_unique` with
`new (std::nothrow)`, and the allocated `unique_ptr` retains the
`nullptr` property.

General block device test: Fix thread stack allocation ...

The test case for multithreaded erase/program/read allocates a few
Thread objects from the heap and starts them. It has a few problems:

* To check that there will be enough heap to start a new thread, the
test case tries to allocate a dummy buffer of the thread's heap size
and then frees it, before starting the thread. Then the thread will
allocate its own stack. Such check is not reliable, because threads
that are already running also perform additional allocation (when
running `test_thread_job()`) and may take away the memory we just
checked.
* When deleting all threads in a loop, the loop boundary misses the
last thread if the last thread object was allocated but not started
(i.e. due to failed thread stack allocation check).

To fix the issues
* Start a thread without any allocation test. Following the preceding
commit "rtos: Thread: Make stack allocation failure runtime catchable",
`Thread::start()` now returns `osErrorNoMemory` if stack allocation
fails which we can handle.
* Store pointers to all threads in a zero-initialized array, and
free all elements at the end of the test.

CMake: Add option to enable greentea tests ...

Add an option to enable the greentea tests independently from the unit
tests.

We can't just use the typical BUILD_TESTING option to enable greentea
tests. BUILD_TESTING enables unit tests and fetches googletest, which
are compiled for the host. Greentea tests are cross compiled and require
a toolchain file. For this reason we add a new option just to enable
greentea tests, preventing build failures triggered by the unit tests
and googletest.

SFDP: Add unit tests for Sector Map Parameter Table parsing ...

Add tests for `sfdp_parse_sector_map_table()` which currently (at the
time of this commit) supports flash devices with
* no Sector Map Parameter Table (i.e. the whole flash is uniform and
non-configurable)
* a single descriptor in the Sector Map Parameter Table (i.e. the
flash layout is non-configurable and has multiple regions)

Support and unit tests for flashes with multiple configurable layouts
will be added in the future.

Note: The implementation of `sfdp_parse_sector_map_table()` assumes
the table to be valid if read succeeds, so the SFDP reader callback
needs to ensure it reads data correctly or return an error.

SFDP: TestEraseTypeAlgorithm: Move setup into test case ...

The test data `struct mbed::sfdp_smptbl_info smptbl` is only relevant
to `TestEraseTypeAlgorithm` and not shared with other test cases.

SFDP: Set region count to 1 for no sector map ...

A flash device with no sector map table has uniform sectors, and we
treat the whole flash as one region. In this case the function
`sfdp_parse_sector_map_table()` sets the single region's size and high
boundary accordingly, but it lacks setting of region count to 1, so
users of the SFDP parser may not get the correct number of regions.
This commit fixes the issue.

SFDP: Move handling of no sector map into `if` ...

When a flash chip's SFDP table has no sector map, we treat the whole
flash as a single region. As an optimization, this should only be
done if there is indeed no sector map.

Unit tests: Remove redundant CMake target mbed-headers-base ...

Individual libraries' `target_h` stub headers have now all been moved
from `mbed-headers-base` to `mbed-headers-<library>`.

Note: Even though headers previously in `target_h` are technically
stubs/fakes too, they are used by not only unit tests but also regular
libraries when compiled for unit tests, because no target-specific HAL
implementation exists in this case. In order for regular library
sources to pick up `target_h` headers, those headers must

* have the same names as regular headers
* appear first in include paths

This is why those headers are part of `mbed-headers-<library>` and not
`mbed-stubs-<library>`. Before this refactoring, `mbed-headers-base`
was the first in unit tests' include paths.

CMake: unittests: Show all tests in CTest report ...

Previously a test executable was recognised as a single test by CTest.
However, test executables usually contain multiple test cases, the
results of the test cases should be individually reported. With our
previous setup we could miss test case failures that didn't cause the
executable to return an error code.

This commit uses gtest_discover_test to discover all test cases in a
test executable. This enables CTest to match test passes and failures
from the googletest binary output.