Fix various memory warnings and clang format

Giovanni Di Siena authored Mar 31, 2020 and Gigg, Martyn Anthony committed Apr 07, 2020

In places other substitutions have been made, e.g
Clang does not yet specialize std::shared_ptr for T[]. Vector
has been used instead. The operator[] methods were incorrectly
marked const but returning a non-const reference - this has been fixed.
Refs #25842

Runs clang-tidy pass by ref across the codebase to fix-up various
warnings we are seeing in cppcheck

Also updated class_maker.py

re #27319

Update copyright headers in all files

Squashed commit of the following:

* First version of a script to manage copyright statements

re #23468

* Neatened up script, added comments

re #23488

* move script to tools directory

re #23488

* small script changes and a couple of manual file changes

re #23488

* Minor chnage to whitespace detection in regex

re #23488

* Add an excluded directory

re #23488

* remove a repeasted copyright statement in a file

re #23488

* Don't comsume the comment end if it is on the same line

re #23488

* fix error in new copright parsing

re #23488

* remove double copyrifght entry

re #23488

* Improve handling of old copyrights at the start of comments

re #23488

* remove empty comments re #23488

* exclude gsoapgenerated directories

re #23488

* Sort out greedy line matching re #23488

* improve empty comment removal

re #23488

* improve false positives

re #23488

* impressive speedup by limiting regex matching length

re #23488

* remove evil invisible non ascii character

Also upadte the copyright at the same time

re #23488

* resolve multiple copyrights in a single file

re #23488

* resolve an issue with new statement detection

re #23488

* another unprintable unicode character

re #23488

* pep updates and cmake the new copyright fit clang format

re #23488

* update already done new format headers

re #23488

* wrong type of bracket

re #23488

* Update class_maker and friends

re #23488

* Update all copyright statements

re #23488

* clang format re #23488

* flake8 warnings re #23488

* Flake8 warnings re #23488

* Exclude .cmake.in and rb.in files

re #23488

* replace missing line re #23488

* exclude .py.in files as they are flasely recognized as C++

re #23488

* another setp.py.in re #23488

* another .py.in correction re #23488

* Hopefully the last of the .py.in files re #23488

* resolve utf-8 encoding of python files and changed ABINS checksum

re #23488

* updates to unit tests that reference line numbers

re #23488

* remaining unit test files and other fixes

re #23488

Update to clang-format-5 and reformat the codebase 

This uses the -fix option on clang-tidy to automatically fix all
the unused usings declarations that have crept into Mantid.

For muon Nexus v1 files, there is always a one-to-one mapping between
spectrum number and detector ID.

Set detector IDs in workspace so that they are correct in the case that
not all spectra are loaded, e.g. load spectra 1-5, 8-10 then detector IDs
shouldn't be 1-8 but 1-5, 8-10 also.

Add a note to documentation.

re #16628

LoadMuonNexus1 looks for number of good frames (goodfrm) in
run/instrument/beam/frames_good for single-period data. This particular
old MUT file didn't have such an entry, and the absence of goodfrm in the
workspace's run object caused a crash later on.

If frames_good isn't there but frames is, use frames and assume they are good.
Log a warning so that the user is kept informed.

re #16723

Error thrown for multi-period files that have number of grouping entries
= number of spectra. Deal with cases like this.

In the case of the test file, this also fails and there is no IDF for DEVA,
so it falls through to getting the dummy grouping. Add a fix because
the grouping loader doesn't know the correct number of detectors.

re #16396

Deal with case when number of dead times = number of spectra for a
multi-period file. It's safe to assume they are the same for each period.

re #16396

re #16070

If the NeXus file has no grouping or zero grouping, load the grouping
from the IDF. If this fails too, use a dummy grouping. In either case,
log a warning message.

This enables the use of such files in the ALC interface, and means the
behaviour is the same as in MuonAnalysis.

re #14085

As well as setting output property of the LoadMuonNexus algorithm, also add the main field direction
to the workspace as a log. This will help algorithms that have the workspace as input and don't have the file,
so would not otherwise know the field direction.

re #15296

to workspace index or spec num
in some cases spec index has been left.  This is due to either:
 1. refering to the spec_index array in nexus files
 2. indirect code where it would be best addressed by Elliot.

re #15450

re #15450