Update to use new manual.nexusformat.org

[FreddieAkeroyd]

The user manual is being moved from download.nexusformat.org to manual.nexusformat.org and served via a gh-pages branch. The www.nexusformat.org site needs some link updating

[prjemian]

content to be checked:

(bluesky_2020_9) prjemian@poof ~/.../NeXus/wiki $ git grep download | grep nexusformat
content/Latest_News.md:Thursday, October 21, 2010: NeXus Manual moved from the wiki to a *book format*(``http://www.nexusformat.org/Documentation``) (PDF & HTML are available). The revised manual also documents the *class definitions*(``http://download.nexusformat.org/doc/html/ClassDefinitions.html``) in [NXDL](https://manual.nexusformat.org/nxdl.html). Content has been reorganised and divided into a volume containing the [User Manual](https://manual.nexusformat.org/pdf/NeXusManual.pdf) and a volume containing the *Reference Documentation*(``http://download.nexusformat.org/doc/NeXusRefDoc.pdf``).  
content/Latest_News.md:definitions](http://download.nexusformat.org/doc/html/Tutorial.html) has
content/Latest_News.md:Tuesday, April 13, 2010: NeXus API version 4.2.1 has now been released and is available from the [download area](http://download.nexusformat.org/kits/) - see [Nexus\_42\_Release\_Notes](Nexus_42_Release_Notes.html "wikilink") for further information  
content/Latest_News.md:Tuesday, November 28, 2006: A NeXus install kit for Microsoft Windows is [now available](http://download.nexusformat.org/kits/windows) The kit includes the standard NeXus applications as well as libraries for building applications with both [MinGW](http://www.mingw.org/) and Microsoft Visual Studio.  
content/NIAC2012.md:    (Sphinx)``http://download.nexusformat.org/sphinx/``
content/NIAC2012.md:    “NeXus Application Definitions” in ``http://download.nexusformat.org/doc/html/ClassDefinitions.html``
content/NIAC2012.md:    currently available at: ``http://download.nexusformat.org/sphinx/``
content/Nexus_42_Release_Notes.md:documentation](http://download.nexusformat.org/doxygen/html/classNeXus_1_1File.html)
content/Nexus_43_Release_Notes.md:page](http://download.nexusformat.org/kits/nx43testing.shtml). Issues
content/TOFRaw.md:(2MB)](http://download.nexusformat.org/TOFRAW/examples/hrp08639.nx4),
content/TOFRaw.md:(2MB)](http://download.nexusformat.org/TOFRAW/examples/hrp08639.nx5) and
content/TOFRaw.md:[XML(16MB)](http://download.nexusformat.org/TOFRAW/examples/hrp08639.xml)
content/TOFRaw.md:DTD](http://download.nexusformat.org/TOFRAW/examples/TOFRAW.xml).
content/Telco_20151215.md:download.nexusformat.org/kits. Only useful stuff remaining there would
content/Telco_20160628.md:        data](https://duckduckgo.com/?q=%22signal+data%22+site%3Ahttp%3A%2F%2Fdownload.nexusformat.org%2Fdoc%2Fhtml&t=ffsb&ia=web):
content/Telco_20160628.md:        <https://duckduckgo.com/?q=%22signal+data%22+site%3Ahttp%3A%2F%2Fdownload.nexusformat.org%2Fdoc%2Fhtml&t=ffsb&ia=web>

[prjemian]

This all looks like history. Do we want to re-write history?

[prjemian]

Checking for manual and nexusformat shows the changes are complete:

(bluesky_2020_9) prjemian@poof ~/.../NeXus/wiki $ git grep manual | grep nexusformat
content/2014_How_to_find_default_data.md:[motivations](https://manual.nexusformat.org/motivations.html)
content/2014_How_to_find_default_data.md:plotting](https://manual.nexusformat.org/motivations.html#simpleplotting).
content/2014_How_to_find_default_data.md:plotted](https://manual.nexusformat.org/datarules.html#find-plottable-data)
content/ActiveProjects.md:[NeXus Mailing List](https://manual.nexusformat.org/mailinglist.html) for
content/CodeCamp2020.md:* We are looking to [publish the manual through GitHub Pages](https://github.com/nexusformat/definitions/issues/663): [https://manual.nexusformat.org](https://manual.nexusformat.org)
content/CodeCamp2020.md:exampledata | [Can we remove the file trees from the readme files as they are out of date and need to be manually updated](https://github.com/nexusformat/exampledata/issues/10) | Done
content/CodeCamp2020.md:definitions | [Is use of UPPER case names described in the manual?](https://github.com/nexusformat/definitions/issues/700) | Done
content/CodeCamp2020.md:definitions | [DATASET_errors naming convention should appear in manual](https://github.com/nexusformat/definitions/issues/721) | Done
content/CodeCamp2020.md:definitions | [PDF manual does not build](https://github.com/nexusformat/definitions/issues/720) | Done
content/CodeCamp2020.md:definitions | [Makefile can't build the PDF manual](https://github.com/nexusformat/definitions/issues/732) | Done
content/Facilities.md:list](https://manual.nexusformat.org/mailinglist.html).
content/Latest_News.md:Thursday, October 21, 2010: NeXus Manual moved from the wiki to a *book format*(``http://www.nexusformat.org/Documentation``) (PDF & HTML are available). The revised manual also documents the *class definitions*(``http://download.nexusformat.org/doc/html/ClassDefinitions.html``) in [NXDL](https://manual.nexusformat.org/nxdl.html). Content has been reorganised and divided into a volume containing the [User Manual](https://manual.nexusformat.org/pdf/NeXusManual.pdf) and a volume containing the *Reference Documentation*(``http://download.nexusformat.org/doc/NeXusRefDoc.pdf``).  
content/Latest_News.md:definitions](https://manual.nexusformat.org/classes/applications/)
content/NAPI_Routines.md:documentation](https://manual.nexusformat.org/doxygen/html-c/)
content/NIAC2020minutes.md:There was a discussion arpound NXptychography, this mainly related to how th ebeam centre should be stored - in NXdetector or using NXtransformations. RO asked if there were any examples of NXtransformations, there are some details on the wiki https://manual.nexusformat.org/design.html#coordinate-transformations but MK will locate a previous presentation he did on the subject. PJ will take back a recommendation to the group for https://github.com/nexusformat/NIAC/issues/53 but further work may be done in the Code CAmp on clarifying the documentation. There is code available in the CBF library to do the necessary maths for transformations.    
content/NIAC2020minutes.md:Reserved prefixes and suffixes were discussed next https://github.com/nexusformat/definitions/issues/769 - reserving "nx" for use by the NIAC is one long standing example, but other communities may wish to reserve a prefix/suffix too. A table will kept in the user manual detailing these and their owners, there will be a NIAC vote to approve the current list. It was also suggested that NIAC be asked to delegate additions (but not removals) to the table to Teleconference meetings. 
content/NIAC2020minutes.md:Discussed https://github.com/nexusformat/NIAC/issues/68 (use NX_DATE_TIME rather than NX_CHAR for file_time and file_update_time in NXroot). NeXus has always said to use ISO8601 for datetime, so this is just bringing the definition in line with the manual. Changed was merged as effectively updating documentation. There was a discussion about timezones, which are not mandatory in ISO8601 - if none are specified local time is assumed. It was agreed to update the manual to say that supplying a timezone was recommended, this avoids issues if e.g. daylight saving time changes during an experiment. 
content/NIAC2020minutes.md:The future on the NeXus C API (NAPI) was discussed https://github.com/nexusformat/NIAC/issues/64 MK gave a brief overview of the hisotory oin the interface and how it simplified the generation of files when HDF4 was the main format. This library has been marked as bugfix only in the documentation, and there are some outstanding issues and pull requests to fix. Some of the issues related to incompatibilitties with newer version of packages such as MXML, and potentially HDF5 1.12  It was agreed that MK and FA would consult the nexus mailing list as to their usage and of NAPI, it may be possible to drop support for e.g. HDF4 or XML from NAPI that would aid future maintenance. RO mentioned that the examples in the user manual use the NAPI a lot. It was agreed the code camp should also revisit the examples in the user manual and makle sure it is clear NAPI is receiving minimal support and provide equivalent HDF5 native API c/c++ examples. We should also update examples generating or referring to HDF4 in the manual, it should only be referenced in the history section. HB pointed out that HDF4 is only minimally supported by the HDF group.  
content/NIAC2020minutes.md:Several members present, in particular AB and RB, were interested in investigaing its usage on future upcoming projects, but many people present had already invested heavily in h5py based approaches. It was agreed that the NeXus manual examples should be updated to show how to read/write files using both nexusfromat and h5py, the simpler interface of nexusformat could be useful to many users. The example updating will be done at the upcoming code camp. BW also noted that the package is not mentioned on the nexus utilities page and will be added there too.   
content/NXgeometry_and_NXshape_-_documentation_and_review.md:*[NXgeometry](https://manual.nexusformat.org/classes/base_classes/NXgeometry.html)*
content/NXgeometry_and_NXshape_-_documentation_and_review.md:-   <https://manual.nexusformat.org/design.html#nexus-coordinate-systems>
content/NXgeometry_and_NXshape_-_documentation_and_review.md:*[NXtranslation](https://manual.nexusformat.org/classes/base_classes/NXtranslation.html)*
content/NXgeometry_and_NXshape_-_documentation_and_review.md:*[NXorientation](https://manual.nexusformat.org/classes/base_classes/NXorientation.html)*
content/NXgeometry_and_NXshape_-_documentation_and_review.md:*[NXshape](https://manual.nexusformat.org/classes/base_classes/NXshape.html)*
content/Telco_20160510.md:        <https://manual.nexusformat.org/classes/base_classes/NXdata.html>
content/Telco_20160614.md:        [NXlog](https://manual.nexusformat.org/classes/base_classes/NXlog.html)
content/Telco_20160614.md:        [NXentry](https://manual.nexusformat.org/classes/base_classes/NXentry.html)
content/Telco_20160614.md:        [NXnote](https://manual.nexusformat.org/classes/base_classes/NXnote.html)
content/Telco_20160614.md:        [NXentry](https://manual.nexusformat.org/classes/base_classes/NXentry.html)
content/Telco_20160628.md:        text](https://manual.nexusformat.org/classes/index.html)
content/Telco_20161123.md:        manual](https://github.com/nexusformat/definitions/issues/277)
content/Telco_20170308.md:-   Questions below from Dectris (Andreas - Tobias edited for markdown) in preparation of the [HDRMX Meeting](https://indico.maxiv.lu.se/event/233/overview). For convenience here are links to [NXdetector](https://manual.nexusformat.org/classes/base_classes/NXdetector.html#nxdetector) and [NXmx](https://manual.nexusformat.org/classes/applications/NXmx.html#nxmx).
content/Telco_20180418.md:* [Add new geometry definitions](https://github.com/nexusformat/definitions/pull/601): Agreed that `<choice>` is the best approach here, rather than fudging this in some other way. Needs changes to the rendering of the manual and the validation tool. MK volunteers to do the latter. PJ shall be approached for the NXDL work.
content/Telco_20190207.md:P.S. The currentl published versions of [NXmx](https://manual.nexusformat.org/classes/applications/NXmx.html#nxmx "wikilink") and [NXdetector](https://manual.nexusformat.org/classes/base_classes/NXdetector.html#nxdetector "wikilink") both provide a "pixel_mask" field that takes a 32-bit pixel mask (and have for over 5 years), so this issue seems to be just about clearly communicating the "old way" vs "new way". 
content/Telco_20190911.md:AB points out that his recent changes to [NXmx](https://github.com/nexusformat/definitions/commit/6e837341abbe3f61a68b65f6d441f9f77c4228de) adds further detail to beam_center_x and beam_center_y than is present in [NXdetector](https://manual.nexusformat.org/classes/base_classes/NXdetector.html). BW responded that while it is not ideal to have diverging documentation, an application definition can make some deviations when needed.
content/Telco_20191107.md:      * For example, the [Manual](https://manual.nexusformat.org/user_manual.html)
content/Telco_20200424.md:       * [NeXus class path](https://manual.nexusformat.org/design.html#index-15) to specify hierachy position
content/index.md:* [User Manual](https://manual.nexusformat.org/user_manual.html):
content/index.md:  * [Introduction](https://manual.nexusformat.org/introduction.html) to the concepts behind the NeXus data format
content/index.md:  * [Design](https://manual.nexusformat.org/design.html): The hierarchical design of NeXus files
content/index.md:  * [NeXus Class Definitions](https://manual.nexusformat.org/classes/index.html): description of each NXDL specification
content/index.md:    * [base classes](https://manual.nexusformat.org/classes/base_classes/index.html): components that might be used in any NeXus data file
content/index.md:    * [application definitions](https://manual.nexusformat.org/classes/applications/index.html): layout specifications for a specific purpose
content/index.md:    * [contributed definitions](https://manual.nexusformat.org/classes/contributed_definitions/index.html): propositions from the community
content/index.md:  * [Utilities](https://manual.nexusformat.org/utilities.html): Software applications that browse, plot, and analyze NeXus data
content/index.md:  * [FAQ](https://manual.nexusformat.org/faq.html): Commonly asked questions about NeXus
content/index.md:* [Mailing Lists](https://manual.nexusformat.org/mailinglist.html)

[prjemian]

@FreddieAkeroyd Close if you agree.