An interesting side-effect of this course - I got _really_ good at using a console/command prompt and handling text with vim and pipes and filters and other text manipulation. I think this has helped me me productive at my jobs way more than I thought it would :)
Unix Network Programming - Stevens 
 RHCSA & RHCE Training and Exam Preparation Guide by Asghar Ghori. This book will help insure you know your stuff as your system engineer/administrator wise.
 A Practical Guide to Linux Commands, Editor and Shell Programming Third Edition. This book will cover the majority of what you would need and want to know when connecting to a remote linux system over ssh.
If you want to get under the hood and become an expert, the following books should help get you started:
 Advanced Programming in the UNIX Environment
 The Linux Programming Interface: A Linux and UNIX System Programming Handbook
 Linux Kernel Development 3rd Edition
To get a nice general overview and get up and going quickly:
 How Linux works: What every superuser should know
 The Linux Command Line
 Python Crash Course
 Automate the boring stuff with Python. This is a great book to help you think about how to automate most of the repetitive things you will end up doing on a regular basis.
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> A secure coding standard form CERT should focus entirely on describing conventions and program properties that do not already follow from the standard as a matter of correctness.
from CERT 1.7
"The wiki also contains two platform-specific annexes at the time of this writing; one annex for POSIX and one for Windows. These annexes have been omitted from this standard because they are not part of the core standard."
So while the CERT does use some examples from system interfaces its not a standard for programming the system interfaces for POSIX or Windows. It looks like there trying to limit the standard to ISO C. The examples you gave fall into the system interface category. POSIX is huge and the same for Windows, much bigger then ISO C.
I think in order to explain conventions for a system interface you really need a longer form publication like a book. So you can take 50 pages to describe an interface and how to use it and show examples etc.
The best way that I have found to figure this stuff out is the standard way. You get a copy of all the relevant standards as a foundation, ISO, POSIX, Window and stuff like CERT. Then you you get some of the system programming books (listed below). Then you find get some good reference code that show best practice. usually code from the operating system or utilities. Lastly read all the compiler docs and tool docs to set up the best code analysis framework you can.
These are a few system programming books that I use.
(best intro book) GNU/Linux Application Programming
UNIX Systems Programming
Advanced Programming in the UNIX Environment
Windows System Programming
The Linux Programming Interface
edit: I'm not sure your skill level, you may have seen all of those but I posted them regardless. There is a lot of security and convention in those books.
The Linux Programming Interface:
Advanced Programming in the UNIX Environment:
A not-too-distant third choice, Linux System Programming:
1. The TCP/IP Guide: A Comprehensive, Illustrated Internet Protocols Reference. http://www.amazon.com/The-TCP-Guide-Comprehensive-Illustrate...
2. Advanced Programming in the UNIX Environment http://www.amazon.com/Programming-Environment-Addison-Wesley...
3. A systems programming language- I choose golang.
5. SSH, The Secure Shell: The Definitive Guide: The Definitive Guide http://www.amazon.com/SSH-Secure-Shell-Definitive-Guide-eboo...
https://github.com/onetrueawk/awk - UNIX philosophy of small tools, DSLs, CS theory: state machines / regular expressions, Thompson algorithm ...
https://github.com/mirrors/emacs - Both a program and a VM for a programming language, hooks, before/after/around advices, modes, asynchronous processing with callbacks, ... Worth to think of challenges of designing interactive programs for extensibility.
https://github.com/rails/rails - Metaprogramming DSLs for creating powerful libraries, again a lesson in hooks (before_save etc.), advices (around_filter etc.), ...
https://github.com/git/git - The distributed paradigm, lots of CS theory again: hashing for ensuring consistency, DAGs everywhere, ... By the way, the sentence "yet the underlying git magic sometimes resulted in frustration with the students" is hilarious in the context of a "software architecture" course.
One of computer algebra systems - the idea of a http://en.wikipedia.org/wiki/Canonical_form
One of computer graphics engines - Linear algebra
There are loads of things one can learn from those projects by studying the source in some depth, but I can't think of any valuable things one could learn by just drawing pictures of the modules and connecting them with arrows. There are also several great books that explore real software design issues and not that kind of pretentious BS, they all come from acknowledged all-time master software "architects", yet all of them almost never find diagrams or "viewpoints" useful for saying the things they want to say, and they all walk you through real issues in real programs:
To me, the kind of approach pictured in the post, seems like copying methods from electrical or civil engineering to appear more "serious", without giving due consideration to whether they really are helpful for anything for real-world software engineering or not. The "software engineering" class which taught those kind of diagram-drawing was about the only university class I did not ever get any use from, in fact I had enough industry experience by the point I took it that it just looked silly.
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