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 

(Both old and new style commands)

After a run is aborted, all previous entries in the "running" log must
be changed to false.

re #17924

The extractToEOL Kernal namespace method has been moved to the Kernal::Strings namespace where it makes more sense to be alongside other string and ascii stream methods

The change was made because of the difficulties i was having with the binary files stream provided by the FileDescriptor.

Refs #9059

This reverts commit ffdc611a.

This reverts commit 069f60c1.

Add two additional ICP conditions.

If the total duration of the differences of the log values
is 0.0 then just use the first log value.

Not sure this is the best thing to do, ideally meanTime()
should be able to cope itself.

refs #6760

Introduced a helper class to perform this stuff and tidy up a lot
of copied code.

Ensures that clone can return the concrete type.