Convert license tags to SPDX identifiers

This commit also converts our own copyright headers to directly use
SPDX, but leaves all other copyright header intact, only adding the
SPDX ident. As far as possible this commit also merges multiple
Data61 copyright statements/headers into one for consistency.

manual: parse all doxygen xml for refdict

Previously the manual would only parse the doxygen for a single xml
file, which meant references to symbols on other files would break.
Parse all doxygen files when constructing the ref dict to fix this.

python2 --> python3

Update all scripts and build system to call python3, given python2's
upcoming doom. Use sys.maxsize instead of sys.maxint in one script
(maxint does not exist in python3).

style: run autopep8 on python files

parse_doxygen: Removed tab in Markdown doc format

Removed a trailing tab character in the Markdown API doc format
string.

manual: add missing newline

fixes a missing new line in generated markdown

manual: label object groups in parse_doxygen_xml.py

This change adds a label to the latex generated object groups.

manual: group generated API methods by object type

This change generates doxygen groups for each object type, which allows us to create sections in
output documents for each object. This has the advantage that we can later label those sections and
link to them from the main document. Additionally, it improves nagivation of the API docs.

manual: use int level in parse_doxygen_xml.py

The level argument to parse_doxygen_xml.py was previously a latex section header (either subsection
or subsubsection). This change converts the argument to numerical which is more robust and is not
limited to 2 specific levels.

This change
- alters the level argument to be an int, where 0 = highest level header,
- removes the translation of latex header to markdown,
- adds a new 'level_to_header' function to the generator class, which translates the level number
to a header for that specific output type.

manual: Added command line option for Markdown

Added a command line option for the user to specify the output
format i.e markdown or latex. The command option is used to either
create a Latex or Markdown class.

manual: Updated comments

Minor comment changes to the parse_doxygen_xml.py script.

manual: Markdown Generator Implementation

Added Markdown Generator implementation. This is a child class
to the Generator class. The Markdown generator class overrides
specific parsing table elements and methods to achieve Markdown
specific output, similar to the Latex Generator.

manual: Updated escape character regex

Updated the text_escape function to regex escape characters in the
generators escape set. This is for the case when a generators
special character set collides with regex's special character
set.

manual: Added <docref> XML Tag to Doxygen

Introduced a new Doxygen XML tag '<docref>'. The intention of
this tag is to indicate a section of text in the Doxygen XML that
will contain a reference to another section in the Manual e.g.
"See \autoref<sec:x>". As other generation formats aren't aware of
other chapters/sections in the manual, the <docref> encapsulation
allows it to omit the text from the output. The Latex generator
has been modified to continue parsing the 'docref' contents.

manual: Added "heading" field to ref_dict

Updated the reference dictionary with a heading field. This is
the heading title given to the api doc section.

manual: Added "original_name" field to ref_dict

Updated the reference dictionary with a non text escaped name
field. This is in case the generator doesn't need the name field
text escaped.

manual: Parameterised escape in 'parse_prototype'

The option to escape the text when parsing the prototype can be
specified to the parse_prototype function. Markdown does not
require special C code characters to be escaped.

manual: Generalised param_string generation

Moved Latex specific param string generation out of the Generator
class. Added functions to generate the desired param string
format that the Latex class can then override.

manual: Generalised Generator Class

Generalised the Generator class, removing Latex specific format
code. Generator class returns empty or plain text when used
by itself.

manual: Added LatexGenerator Child class

Implemented LatexGenerator child class which extends the
Generator class. The Latex class overrides methods of the
Generator with Latex specific format. Currently a lot of
duplication between Generator and Latex class, need to
generalise the Generator class.

manual: Renamed methods in Generator class

Renamed select methods to more generic names that don't suggest
they create Latex output.

manual: Moved location of get_parse_table function

Code tidying. Moved get_parse_table to the top of the class
implementation to make it more clear/distinct from the other
methods.

manual: Moved escape regex into latex_escape func

New generator classes are expected to override the ESCAPE_PATTERNS
variable. Moving the regex into an object method allows it to use
the overriden escape patterns.

manual: Parameterised the generator class

Parameterised the generator class for the
'generate_general_syscall_doc' method. This will allow the caller
to pass the desired generator to the function.

manual: Created generate_api_doc methods

Moved api doc string format into a seperate function within the
Generator class. This will allow new generators to override the
function with their own api doc format.

manual: Moved functionality into Generator class

Moved the parsing functionality into a object. The goal is to
refactor the script into an object model such that we can extend
and override parsing functions to output the doxygen to different
formats. Additionally updated the various methods and variable
accesses to use 'self' inorder to work in the new object oriented
paradigm.

manual: Moved parse table to function

The parse table has been moved to a function. Updated use
of the PARSE_TABLE to call the function instead.

manual: fix python script to be python3 compatible

manual: allow non sec autorefs

Previously anything in an autoref block was assumed to reference
a section, which isn't true. Change 'sec' to 'label' and move the
'sec' prefix into the label itself.

manual: fix double escaping bug

manual: support for itemized lists

manual: fix script licenses

manual: appease pylint

manual: refactor + cleanup parse_doxygen_xml.py

- use 'recursive=False' rather than 'content' to only search children
- use a parse table instead of if a long if/else
- fix nested lists
- use get_text from beautiful_soup rather than home brewed
- don't call latex_escape explicitly

SELFOUR-962: allow API level description in manual

SELFOUR-961: allow lists in API docs

this change

- converts ordered doxygen lists to enumerate
- also wraps the benchmark config names in texttt

manual: use BeautifulSoup in parse_doxygen_xml

Use BeautifulSoup instead of minidom, for more powerful features

manual: Explicitly say TODO where doc is missing

manual: Comments to docstrings

manual: Include prototypes for undocumented fns

manual: More robust hanlding of xml errors

When generating latex from doxygen-generated xml, if an expected element
is not found in the xml, raise a meaningful exception.

manual: Improve handling of return type docs

If no documentation is provided for the return value of a function, the
documentation generator will attempt to infer the documentation based on
the return type.

manual: Handle case where api has no methods

manual: Parameterize \apidoc cmd with section type

manual: Fixed bug where params out of order in doc

JIRA: SELFOUR-606

manual: More tags recognised by doxy xml parser

JIRA: SELFOUR-606

Syscalls docs in manual generated by doxygen

This adds a dummy header with syscall prototypes with doxygen comments.
The build process for the manual includes parsing these comments using
doxygen. Doxygen produces an xml file which is parsed by a script to
generate latex which is included in the manual. This approach was chosen
over doxygen's native latex output to gain greater control over the
formatting of the generated documentation, and to take advantage of
existing api-formatting support in the sel4 manual.

Related issue: SELFOUR-606