Readme 404 fix

[missing-user]

Suggested fix for #205 the broken URLs in the readme.

• Also made minor fixes related to the doxygen grouping, where some routines that produce hidden files weren't part of grp_output
• Added the citations file
• Generally cleaned up the README a bit, added headings and the SPEC logo

[smiet]

Thank you so much!

I see that there On the issue there were a few requests:
-> separate the references into the citelist, containing only

• https://iopscience.iop.org/article/10.1088/0741-3335/54/1/014005
• https://iopscience.iop.org/article/10.1088/1361-6587/ab9a61/meta

-> and a biblography with the other papers ("A list of publications using SPEC are in our bibliography section"

• https://doi.org/10.1063/1.4967709
• https://doi.org/10.1017/S0022377821000520
• https://doi.org/10.1063/1.4944818
• https://doi.org/10.1063/1.4931094
• https://doi.org/10.1063/1.4906888
• https://doi.org/10.1063/5.0009110
• https://doi.org/10.1017/S0022377823000934
• https://doi.org/10.1017/S0022377817000861
• https://doi.org/10.1017/S0022377823000910
• https://doi.org/10.1063/1.5091765
• https://dx.doi.org/10.1088/1741-4326/ad39d9

And link to it.

Warmest regards,
Chris