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Why do standard classes sometimes have seemingly unrelated methods?

While studying the standard Java library and its classes, i couldn't help noticing that some of those classes have methods that, in my opinion, have next to no relevance to those classes' cause.
The methods i'm talking about are, for example, Integer#getInteger, which retrieves a value of some "system property", or System#arraycopy, whose purpose is well-defined by its name.
Still, both of these methods seem kinda out of place, especially the first one, which for some reason binds working with system resources to a primitive type wrapper class.
From my current point of view, such method placement policy looks like a violation of a fundamental OOP design principle: that each class must be dedicated to solving its particular set of problems and not turn itself into a Swiss army knife.
But since i don't think that Java designers are idiots, i assume that there's some logic behind a decision to place those methods right where they are. So i'd be grateful if someone could explain what that logic really is.
Thanks!
Update
A few people have hinted at the fact that Java does have its illogical things that are simply remnants of a turbulent past. I reformulate my question then: why is Java so unwilling to mark its architectural flaws as deprecated, since it's not like that the existing deprecated features are likely to be discontinued in any observable future, and making things deprecated really helps refraining from using them in newly created code?

This is a good thing to wonder about. I know about more recent features (such as generics, lambda's etc) there are several blogs and posts on mailing lists that explain the choices made by the library makers. These are very interesting to read.
In your case I expect the answer isn't too exiting. The reason they were made is hard to tell. But both classes exist since JDK1.0. In those days the quality of programming in general (and also Java and OO in particular) was perhaps lower (meaning there were fewer common practices, library makers had to invent many paradigms themselves). Also there were other constraints in those times, such as Object creation being expensive.
Many of those awkwardly designed methods and classes now have a better alternative. (See Date and the package java.time)
The arraycopy you would expect to be added to the Arrays class, but unfortunately it is not there.
Ideally the original method would be deprecated for a while and then removed. Many libraries follow this strategy. Java however is very conservative about this and only deprecates things that really should not be used (such as Thread.stop(). I don't think a method has ever been removed in Java due to deprecation. This means it is fairly easy to upgrade your software to a newer version of Java, but it comes at the cost of leaving some clutter in the libraries.
The fact that java is so conservative about keeping the new JDK/JRE versions compatible with older source code and binaries is loved and hated. For your hobby project, or a small actively developed project upgrading to a new JVM that removes deprecated functions after a few years is not too difficult. But don't forget that many projects are not actively developed or the developers have a hard time making changes securely, for instance because they lack a proper regression test. In these projects changes in APIs cost a lot of time to comply to, and run the risk of introducing bugs.
Also libraries often try to support older versions of Java as well as newer version, they will have a problem doing so when methods have been deleted.

The Integer-example is probably just a design decision. If you want to implicitly interpret a property as Integer use java.lang.Integer. Otherwise you would have to provide a getter method for each java.lang-Type. Something like:
System.getPropertyAsBoolean(String)
System.getPropertyAsByte(String)
System.getPropertyAsInteger(String)
...
And for each data type, you'd require one additional method for the default:
- System.getPropertyAsBoolean(String, boolean)
- System.getPropertyAsByte(String, byte)
...
Since java.lang-Types already have some cast abilities (Integer.valueOf(String)), I am not too surprised to find a getProperty method here. Convenience in trade for breaking principles a tiny bit.
For the System.arraycopy, I guess it is an operation that depends on the operating system. You probably copy memory from one location to another in a very efficient way. If I would want to copy an array like that, I'd look for it in java.lang.System

"I assume that there's some logic behind a decision to place those
methods right where they are."
While that is often true, I have found that when somethings off, this assumption is typically where you are mislead.
A language is in constant development, from the day someone proposes a new language to the day it is antiquated. In between those extremes are some phases that the language, go through. Especially if someone is spending money on it and wants people to use it, a very peculiar phase often occurs, just before or after the first release:
The "we need this to work yesterday" phase.
This is where stuff like this happens, you have an almost complete language, but the programmers need to do something to to show what the language can do, or a specific application needs a feature that was not designed into the language.
So where do we add this feature?
- well, where it makes most sense to that particular programmer who's task it is to "make it work yesterday".
The logic may be that, this is where the function makes the most sense, since it doesn't belong anywhere else, and it doesn't deserve a class of its own. It could also be something like: so far, we have never done an array copy, without using system.. lets put arraycopy in there, and save everyone an extra include..
in the next generation of the language, people will not move the feature, since some experienced programmers will complain. So the feature may be duplicated, and found in a place where it makes more sense.
much later, it will be marked as deprecated, and deleted, if anyone cares to clean it up..

Combining Java and C without gcj -- move C to Java or Java to C?

First, I have no experience doing this. But like the beginning of any good program, I have problem that I need to fix, so I'm willing to learn.
So many of you are probably already familiar with pdftk, the handy utility for handling various pdf-related tasks. So far as I can tell, most of these features are available in much newer, lighter libraries/extensions, except the one I need (and probably the only reason it still exists): merging form data files (fdf and xfdf) with a form PDF and getting a new file as the output.
The problem is that my server doesn't have gcj, which is fundamental to build/compile pdftk. I don't know if it's because I'm on Solaris or if it's for some other sysadmin-level reason, but I'm not getting gcj anytime soon. And there are no pre-compiled binaries for Solaris as far as I can find.
So I'm thinking that the MAKE file and C code can be rewritten to import the Java library (very ancient version of itext) directly, via javac.
But I'm not sure where to really start. All I know is:
I want a binary when I'm done, so that there won't be a need for a Java VM on every use.
The current app uses GCJ.
So my first thought was "Oh this is easy, I can probably just call the classes with some other C-based method", but instead of finding a simple method for doing this, I'm finding tons of lengthy posts on the various angles that this can be approached, etc.
Then I found a page on Sun's site on how to call other languages (like C) in a Java class. But the problems with that approach are:
I'd have to write a wrapper for the wrapper
I'd probably be better off skipping that part and writing the whole thing in Java
I ain't ready for that just yet if I can just import the classes with what is already there
I'm not clear on if I can compile and get a binary at the end or if I'm trapped in Java being needed every time.
Again, I apologize for my ignorance. I just need some advice and examples of how one would replace GCJ dependent C code with something that works directly with Java.
And of course if I'm asking one of those "if we could do that, we'd be rich already" type questions, let me know.

I'm not sure what you are looking for exactly, so I provided several answers.
If you have java code that needs to run, you must:
Run it in a jvm. You can start that vm within your own custom c-code, but it is still using a jvm
Rewrite it in another language.
Compile with an ahead-of-time compiler (eg gcj)
Incidentally, you could compile a copy of gcj in your home folder and use that. I believe the magic switch is --enable-languages=java,c (see: here for more)
If you have c-code you want to call from java, you have four options:
Java Native Interface (JNI). It seems you found this
Java Native Access (JNA). This is slower than JNI, but requires less coding and no wrapper c-code. It does require a jar and a library
Create a CLI utility and use Runtime.Exec(...) to call it.
Use some sort of Inter Process Communication to have the Java code ask the c-code to perform the operation and return the result.
Additional platform dependent options
Use JACOB (win32 only: com access)

I am not sure if I understand what you are looking for.
If you are looking to incorporate the C code into Java to make a native binary without the gcj, I think you are out of luck. You can include the C in Java, but it would be a primarily Java program meaning you would need the JVM on each run. Is there anything stopping you from compiling the gcj yourself?

Bootstrap loader using java

Normally boot strap loaders are written using assembly languages.
Is it possible to dot it using java with native interface.

There are some possible solutions:
It exists hardware, that is able to
execute Java-bytecode.
Also you can compile Java-code to
native code with different
compilers.
Finally you can have a mini-loader, that
starts the rest of the process in
Java.
Neither of this solutions is easy or does make too much sense. But possible - yes.
For completeness: JNode is a project targeting to create a PC-Operating-system in Java.
Also answers to this question may be helpful. It ask for device-drivers in Java, and that's not completely the same question, but some of the solutions presented in the answers may be helpful with your question too.

I don't want to say an outright no, because I'm sure if I did someone would come up with a way of doing it, but this would certainly be VERY difficult (and possibly fruitless).
For Java to run on a JVM, you'd need to natively bootstrap a sufficient amount of the OS natively that then switching to java would be a bit of a waste of time (it really wouldn't accomplish much other than adding complexity).
There are devices that can "natively" run bytecode where it's conceivably possibly, but I don't think that's viable most of the time.

Of course it is. A better question would be whether it is practical or not, and if it would offer any benefits worth the implementation time compared to existing methods.

#Mnementh mentioned JNode. For the record, JNode uses GRUB as its bootstrap loader.
I agree with #Mnementh that implementing a boot loader in Java would be technically possible though probably difficult. But my question to the OP is "why would you want to do it?". I don't see the point.

How to deal with the most common classes missing on J2ME

I'm trying to code an application which runs un different java platforms like J2SE, J2ME, Android, etc. I already know that I'll have to rewrite most of the UI for each platform, but want to reuse the core logic.
Keeping this core portable involves three drawbacks that I know of:
Keeping to the old Java 1.4 syntax, not using any of the nice language features of Java 5.0
only using external libraries that are known to work on those platforms (that is: don't use JNI and don't have dependencies to other libs which violate this rules)
only using the classes which are present on all those platforms
I know of ways to overcome (1): code in 5.0 style and automatically convert it to 1.4 (retroweaver - haven't tried it yet, but seems ok).
I think (2) is a problem that I just have to accept.
Now I'd like to know what's the best workarround for (3), especially collection classes, which I miss the most. I can think of those:
Most programmers I know just don't use Set, Map, List, etc. and fallback to Vector and plain Arrays. I think this makes code ugly in the first place. But I also know that the right choice between TreeSet/Hashset or LinkedList/ArrayList is crucial for performance, and always using Vector and Arrays can't be right.
I could code my own implementations of that classes. This seems to be reinventing the wheel, and I think I could not do it as good as others have done.
Since Java is open source, I could grab the sourcecode of the J2SE Collections framework and include into my application when building for J2ME. I don't know if this is a good idea, though. Pherhaps there are good reasons not to do this.
Maybe there already are libraries out there, which rebuild the most important features of the collections framework, but are optimized for low end systems, pherhaps by not implementing functionality that is used infrequently. Do you know any?
Thanks for your answers and opinions!
Edit: I finally found a (complex, but nice) solution, and I thought by providing my own answer and accepting it, the solution would become visible at the top. But to the contrary, my answer is still at the very bottom.

J2ME is brutal, and you're just going to have to resign yourself to doing without some of the niceties of other platforms. Get used to Hashtable and Vector, and writing your own wrappers on top of those. Also, don't make the mistake of assuming that J2ME is standard either, as each manufacturer's JVM can do things in profoundly different ways. I wouldn't worry much about performance initially, as just getting correctness on J2ME is enough of a challenge. It is possible to write an app that runs across J2ME, J2SE and Android, as I've done it, but it takes a lot of work. One suggestion that I'd have is that you write the core of your application logic and keep it strictly to java.lang, java.util and java.io. Anywhere where you're going to be doing something that might interact with the platform, such as the file system or network, you can create an interface that your core application code interacts with, that you have different implementations for the different environments. For example, you can have an interface that wraps up HTTP stuff, and uses javax.microedition.io.HttpConnection with J2ME and java.net.HttpURLConnection on Android. It's a pain, but if you want to maintain an app running on all three of those environments, it can get you there. Good luck.

It's been a while since I asked this question, and I while since I found a nice, working solution for the problem, but I had since forgotton to tell you.
My main focus was the Java Collections Framework, which is part of the java.util package.
I've finally taken the source code of Suns Java 6.0 and copied all the classes that belong to the Collections framework into a project of my own. This was a Java 6.0 project, but I used the jars from J2ME as classpath. Most of those classes that I copied depend on other J2SE classes, so there are broken dependencies. Anyway, it was quite easy to cut those depensencies by leaving out everything that deals with serialization (which is not a priority for me) and some minor adjustments.
I compiled the whole thing with a Java 6 compiler, and retrotranslator was used to port the resulting bytecode back to Java 1.2.
Next problem is the package name, because you can't deliver classes from java.util with a J2ME application and load them - the bootstrap class loader won't look into the applications jar file, the other bootloaders aren't allowed to load something with that package name, and on J2ME you can't define custom classloaders. Retrotranslator not only converts bytecode, it also helps to change name references in existing bytecode. I had to move and rename all classes in my project, e.g. java.util.TreeMap became my.company.backport.java.util.TreeMap_.
I was than able to write actual J2ME application in a second Java 6.0 project which referenced the usual java.util.TreeMap, using the generic syntax to create type-safe collections, compile that app to Java 6.0 byte code, and run it through retrotranslator to create Java 1.2 code that now references my.company.backport.java.util.TreeMap_. Note that TreeMap is just an example, it actually works for the whole collections framework and even for 3rd party J2SE Jars that reference that framework.
The resulting app can be packaged as a jar and jad file, and runs fine on both J2ME emulators and actual devices (tested on a Sony Ericsson W880i).
The whole process seems rather complex, but since I used Ant for build automation, and I needed retranslator anyway, there only was a one-time overhead to setup the collection framework backport.
As stated above, I've done this nearly a year ago, and writing this mostly from the top of my head, so I hope there are no errors in it. If you are interested in more details, leave me a comment. I've got a few pages of German documentation about that process, which I could provide if there is any demand.

We faced exactly this situation in developing zxing. If J2ME is in your list of targets, this is your limiting factor by far. We targeted MIDP 2.0 / CLDC 1.1. If you have a similar requirement, you need to stick to Java 1.2. Java 1.4 language features are definitely not present (like assert) and in general you won't find anything after 1.2 in J2ME.
We did not use external libraries, but, you could package them into your deployed .jar file with little trouble. It would make the resulting .jar bigger, and that could be an issue. (Then you can try optimizers/shrinkers like ProGuard to mitigate that.)
I did end up reimplementing something like Collections.sort() and Comparator since we needed them and they are not in J2ME. So yeah you might consider doing this in cases, though only where necessary.
We used Vector and Hashtable and arrays since there is no other choice, really, in J2ME. I would just use them unless you have a reason not to, and that would be performance I guess. In theory JVM makers are already optimizing their implementation but that doesn't mean you couldn't make a better one... I guess I would be surprised if it is worth it in the vast majority of cases. Just make sure you really need to do this before putting in the effort.

To answer part of your question another collections library would be Javolution which can be built for j2me.

Is BCEL == monkeypatching for java?

a colleague pointed me the other day to BCEL which , as best I can tell from his explanation and a quick read, a way to modify at run time the byte code. My first thought was that it sounded dangerous, and my second thought was that it sounded cool. Then I gave it some more thought and I recalled the codinghorror post on monkey-patching and realized that this was basically the same thing. Has anyone ever used BCEL for anything practical? Am I right that this is basically run time monkey patching, or am I missing something?

From BCEL's FAQ:
Q: Can I create or modify classes
dynamically with BCEL?
A: BCEL contains useful classes in the
util package, namely ClassLoader and
JavaWrapper.Take a look at the
ProxyCreator example.
But monkeypatching is... uhm... controversial, and you probably shouldn't use it if your language doesn't support it.
If you have a good use case for it, may I suggest embbededing Jython?

It's a bit more low-level than classic monkey patching, and from what I read, the classes already loaded into the VM are not updated. It only supports saving it to class files again, not modifying run time classes.

You might look at it as monkey patching. I prefer not to use it (maybe I never faced a good use case for it?), but be familiar with it (to have an idea how Spring and Hibenrate use it and why).

See this realworld example: Jawk - Compiler Module. BCEL is useful for "compilation" ur custom language.

BCEL does not support monkey patching, it just manipulates with bytecode and possibly loads it in a custom classloader. However you can implement monkeypatching on JVM using library like BCEL and Java agent. The Java agent (loaded by -javaagent argument) can access the Instrumentation API and modify loaded classes. It is not hard to implement it via some bridges.
But remember:
I am not sure if having to use -javaagent is something you want.
In any language, monkey patching can lead to badly predictable behavior.
You can modify a method. In theory, you can also add some method, but you need to compile the project against modified (patched) classes. I think this would cause a lot of pain and it is not worth of it. There are alternative languages that support it (e.g. Groovy) or suppport something similar (e.g. implicit conversions in Scala).
It is better to design your API well than to use monkey patching. It may be rather useful for third party libraries.