What good practices, if any, has the agile movement lost?
I am a long time agile advocated but one of the things that bothers me about Agile is that a lot of agile practitioners, especially the younger ones, have thrown out or are missing a whole lot of good (non Scrum, non XP) practices. Alistair Cockburn's style of writing Use Cases springs to mind; orthogonal arrays (pairwise testing) is another.
I read mostly Agile related books and articles and work with mostly Agile folk ... is there anything I'm missing?
在5 - 10年的时间里，看看这些系统在没有人写下为什么做出特定决定以及所有相关人员都离开时如何保持可能性，这可能是有趣的。
is there anything I'm missing?
Yes, I think a lot, but only if you are interested in Softawre Development Processes.
I like this paraphrase:
Each project should be as agile as possible but not more agile.
Not every project can be agile... but I think 80%+ can.
I see Agile as "car of the year". It is very well suited for most of the people, but if you need/want something special, for example car able to speed 300KM/H or car able to carry 20 tons of goods you need something else.
There is also so many cases when one may want something else than "car of the year" that requires a book to write them down :-) I recommend you Agility and Discipline Made Easy: Practices from OpenUP and RUP. In this book you'll find many "missing parts" very well illustrated. The key to understanding is that Agility is only a (requested) property of software development process which sometimes cannot be achieved. The book describes several Key Development Principles (which are basis for RUP) and explains which level of "ceremony" and "iterativeness" follows from using them on different levels of adoption.
An example
Practice: Automate change management and change propagation
In your project you may require very advanced and strict change management and decide to "Automate change management and change propagation" by implementing custom or re-configuring existing tools and by using Change and Control Board.
Effect: This most probably increase level of "ceremony" in your project.
(...) have thrown out or are missing a whole lot of good (non Scrum, non XP) practices.
Scrum is not prescriptive, it's up to you to choose how to do things. In other words, nothing forces you to use User Stories for example (even if User Stories work for lots of teams, there is no consensus) so feel free to use (light) use-cases if you think they are more appropriate in your context. To illustrate this, Jeff Sutherland reported he would never use User Stories again for PDA device projects (they use some kind of "light specifications" in his current company). And the same applies for testing, use whatever works for you. To summarize, if you find XP not flexible enough, use something else... and inspect and adapt.
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