new SqlSessionFactoryBuilder().build(inputStream, properties)

SqlSessionFactory sqlSessionFactory =new SqlSessionFactoryBuilder().build(inputStream, properties);

  public XMLConfigBuilder(InputStream inputStream, String environment, Properties props) {
    this(new XPathParser(inputStream, true, props, new XMLMapperEntityResolver()), environment, props);
  }

this中的处理逻辑：

new XPathParser(inputStream, true, props, new XMLMapperEntityResolver())

org.apache.ibatis.parsing.XPathParser

  public XPathParser(InputStream inputStream, boolean validation, Properties variables, EntityResolver entityResolver) {
    commonConstructor(validation, variables, entityResolver);
    this.document = createDocument(new InputSource(inputStream));
  }

  private void commonConstructor(boolean validation, Properties variables, EntityResolver entityResolver) {
    this.validation = validation;
    this.entityResolver = entityResolver;
    this.variables = variables;
    XPathFactory factory = XPathFactory.newInstance();
    this.xpath = factory.newXPath();
  }

返回一个org.w3c.dom.Document

  private Document createDocument(InputSource inputSource) {
    // important: this must only be called AFTER common constructor
    try {
      DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
      factory.setValidating(validation);

      factory.setNamespaceAware(false);
      factory.setIgnoringComments(true);
      factory.setIgnoringElementContentWhitespace(false);
      factory.setCoalescing(false);
      factory.setExpandEntityReferences(true);

      DocumentBuilder builder = factory.newDocumentBuilder();
      builder.setEntityResolver(entityResolver);
      builder.setErrorHandler(new ErrorHandler() {
        public void error(SAXParseException exception) throws SAXException {
          throw exception;
        }

        public void fatalError(SAXParseException exception) throws SAXException {
          throw exception;
        }

        public void warning(SAXParseException exception) throws SAXException {
        }
      });
      return builder.parse(inputSource);
    } catch (Exception e) {
      throw new BuilderException("Error creating document instance.  Cause: " + e, e);
    }
  }

com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl

    public Document parse(InputSource is) throws SAXException, IOException {
        if (is == null) {
            throw new IllegalArgumentException(
                DOMMessageFormatter.formatMessage(DOMMessageFormatter.DOM_DOMAIN,
                "jaxp-null-input-source", null));
        }
        if (fSchemaValidator != null) {
            if (fSchemaValidationManager != null) {
                fSchemaValidationManager.reset();
                fUnparsedEntityHandler.reset();
            }
            resetSchemaValidator();
        }
        domParser.parse(is);
        Document doc = domParser.getDocument();
        domParser.dropDocumentReferences();
        return doc;
    }

继续org.apache.ibatis.builder.xml.XMLConfigBuilder中的处理：

  private XMLConfigBuilder(XPathParser parser, String environment, Properties props) {
    super(new Configuration());
    ErrorContext.instance().resource("SQL Mapper Configuration");
    this.configuration.setVariables(props);
    this.parsed = false;
    this.environment = environment;
    this.parser = parser;
  }

parser.evalNode("/configuration"):

org.apache.ibatis.parsing.XPathParser
public XNode evalNode(String expression)

  public Configuration parse() {
    if (parsed) {
      throw new BuilderException("Each XMLConfigBuilder can only be used once.");
    }
    parsed = true;
    parseConfiguration(parser.evalNode("/configuration"));//
    return configuration;
  }

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE configuration
        PUBLIC "-//mybatis.org//DTD Config 3.0//EN"
        "http://mybatis.org/dtd/mybatis-3-config.dtd">
<configuration>
    <settings>
        <setting name="logImpl" value="LOG4J"/>
    </settings>
    <typeAliases>
        <package name="com.tangcheng.mybatis.introduction.domain"/>
    </typeAliases>

    <environments default="dev">
        <environment id="dev">
            <transactionManager type="JDBC"></transactionManager>
            <dataSource type="UNPOOLED">
                <property name="driver" value="com.mysql.jdbc.Driver"/>
                <property name="url" value="jdbc:mysql://localhost:3306/mybatis"/>
                <property name="username" value="root"/>
                <property name="password" value=""/>
            </dataSource>
        </environment>
    </environments>

    <mappers>
        <mapper resource="mapper"/> //更改成 <mapper resource="mapper/CountryMapper.xml"/> 错误即可消失
    </mappers>

</configuration>

Caused by: org.apache.ibatis.builder.BuilderException: Error creating document instance.  Cause: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.apache.ibatis.parsing.XPathParser.createDocument(XPathParser.java:259)
	at org.apache.ibatis.parsing.XPathParser.<init>(XPathParser.java:125)
	at org.apache.ibatis.builder.xml.XMLMapperBuilder.<init>(XMLMapperBuilder.java:78)
	at org.apache.ibatis.builder.xml.XMLConfigBuilder.mapperElement(XMLConfigBuilder.java:339)
	at org.apache.ibatis.builder.xml.XMLConfigBuilder.parseConfiguration(XMLConfigBuilder.java:113)
	... 23 more
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)
	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400)
	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
	at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1472)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:994)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:841)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:770)
	at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
	at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:243)
	at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:339)
	at org.apache.ibatis.parsing.XPathParser.createDocument(XPathParser.java:257)
	... 27 more

参考：
http://blog.csdn.net/Yhboom/article/details/75041618