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Use of Bean configuration XML File

I am a new user of Spring framework. I am facing some confusion in understanding the difference between core spring framework and spring boot. As far as I understand, Spring boot is a framework which performs the initial setup automatically (like Setting up Maven dependencies and downloading the jar files) and comes with an embedded Tomcat server which makes it ready to deploy in just one click., Whereas, Spring MVC requires manual setup. All the tutorials that I watched for core spring show bean configuration using bean factory which configures the beans using a .XML file. In Spring boot, this bean configuration file is absent. My question is, what is the use of this bean configuration file? I did not find any legitimate use of this file in making a REST service with spring. I didn't see any use of the Application Context, Bean Factory in creating web application. Can someone point out how can bean factory be used in Spring web apps? Is there any fundamental difference between core spring and spring boot other than the additional components?

The Spring application context is essentially the "pool" of beans (service objects, which include controllers, converters, data-access objects, and so on) and related information that define an application; I recommend the reference introduction. In theory, you can get complicated with the context setup and have hierarchical organization and such, but in most real-world cases you just have a single plain context.
Inside this context you need to install all of the beans that provide the logic for your application. There are several possible ways to do this, but the two main ways are by providing XML files with have directives like bean (define an individual bean) or component-scan (automatically search for classes with certain annotations, including #Controller) and by using Java classes annotated with #Configuration, which can use annotations and #Bean methods.
The XML style is generally older, and newer applications mostly use Java configuration, but both provide entries that are collected into the context, and you can use both simultaneously. However, in any application, you have to provide some way of getting the registration started, and you will typically have one "root" XML file or configuration class that then imports other XML files and/or configuration classes. In a legacy web.xml-based application, you specify this in your servlet configuration file.
Spring Boot is, as you said, essentially a collection of ready-to-go configuration classes along with a mechanism for automatically detecting configurations and activating them. Even this requires a configuration root, though! This is the #EnableAutoConfiguration instruction, frequently used through its composite #SpringBootApplication. The application context and configuration mechanisms work normally once Boot finds them and pulls them in. Spring knows where to get started because you give it an explicit instruction to build a context starting with that entry point, usually with SpringApplication.run(MyApplication.class, args).
The embedded-server configuration just happens to be a particular set of configuration that is really useful and comes with one of the Boot starter packages. There's nothing there that you couldn't do in a non-Boot application.

Need some clarification on Spring Configuration and Initializer

I have been following this tutorial to build my Spring REST API for a project.
http://websystique.com/springmvc/spring-4-mvc-rest-service-example-using-restcontroller/
Now, I have a question. Do i have to create <class_name>Configuration and <class_name>Initializer class for every rest controller that I am going to make ?

The answer is no. Configuration and Initializer classes are application context wide. Those are just another way of configuring the Spring application context (the other is using xml configuration files)

Spring 3 Application Context loading

I am a bit familiar with Spring framework but am still having lots of question concerning use of spring from project architectural view point. Now I am setting up Spring 3 and a Maven web application and am willing to try out all the the fancy component-scan's and autowiring features however this is where I get confused.
I am trying to break the project into sub-modules. And at some point these sub-modules may include something-context.xml in classpath*:resource/META-INF, like for instance when I will want to define a datSource related stuff in a separate module. So that's fine spring let's you load context files from within class-paths of all of the jars.
But here is where it gets vague - say I am using component scan. I am obviously using spring DispatcherServlet and it needs a servlet context to be loaded, and then there is a global application context parameter specified in web.xml contextConfigLocation.
So now servlet context config has a component-scan feature enabled for com.mycom.project.controllers and context loaded in the global contextConfigLocation has a context loaded with component scan feature for package com.mycom.project also searches for classpath*:META-INF/spring/*-context.xml.
So my question is - does this load controller's twice given that component scan is used for a for com.mycom.project.controllers and com.mycom.project? Or is it all loaded into one huge container and the contextConfigLocation parameter for either DispatcherServlet or global declaration is sort of access issue ? As in DispatcherServlet will reach only what's defined in servlet-context.xml but won't be able to use anything else?
And if my assumption is wrong, could I have a suggestion on how to manage multi-module project issues?
Thanks.

Yes, you might run into trouble. See this link for how to solve your problem.
#Service are constructed twice
The way you proceed when creating modules seems valid to me. You have a context.xml file for each module and all will get loaded once you load the application. Your modules are self-contained and can also be used in different environments. That's pretty much the way I'd also do it.

Overwrite configuration for Spring project from outside

I'm developing a Spring application which shall be used by any kind of other application, no matter if that is a Spring project, a web application or even a simple single-class console application. The application who uses my project will just have to add the JAR file with my application.
So my project has a static factory class that gets and returns a bean from its Spring context which acts as an access object to access all public available functions of my project.
That part is already working.
But I need the developer of the application that uses my JAR to be able to overwrite certain configurations in my project without editing the config files in the JAR itself. At the moment those settings should be overwritable:
- the data source and hibernate bean configuration
- the jasypt (encryption) bean configuration
- the log4j settings
How do I make those settings overwriteable with configs from outside the jar?
Greetings
touchdown

Maybe a good solution would be a configuration that the user could override, for this take a look into:
http://static.springsource.org/spring/docs/3.0.x/spring-framework-reference/html/beans.html#beans-java
Specially to #Configuration and #Bean
Maybe you could have a configuration class implemented and the user can override it. After extending the class and overwrite some methods that provides some beans the user shall inform it to your factory that will do nothing else than
new AnnotationConfigApplicationContext(userConfigurationClass);

If you want to replace the complete configuration, than the easyest way would be to have a parametrized factory that takes an alternative configuration file as its argument.
If you need it a bit more fine grain (lets say up to 10 parts), than you can split your application xml in several smaller once, and use again a configurable factory that allows to exchange the smaller xml files.

So I got a solution that is working for me.
I put an general import for override context-XMLs at the bottom of my main application context:
<import resource="classpath*:project/package/config/override/or-*.xml" />
So all the user has to do is to create the package "project/package/config/override" in his classpath (e.g. resource folder) and place matching XML files in it with new bean definitions.

how to load spring without a web container

I have a RESTful service using Jersey/Spring/Tomcat. My question is - is it possible to access the classes within my war from command line (without the web interface)?
The problem is the JDBC connections and some other beans are managed by spring. So how do I load all these beans without the web container?

You can easily initialize application context and load all the classes manually. Here is an example:
ConfigurableApplicationContext applicationContext = new ClassPathXmlApplicationContext("/applicationContext.xml");
YourBean yourBean = applicationContext.getBean("yourBean", YourBean.class);
applicationContext.close();

Classes in a WAR archive are tricky, because you'll have to tell the ClassLoader to look inside WEB-INF/classes and WEB-INF/lib/*.jar . Sounds non-trivial to me...