Documentation for JIRA 4.3. Documentation for other versions of JIRA is available too. 

The 'JIRA installation directory' is the directory into which the JIRA application files and libraries have been unpacked (unzipped) when JIRA was installed. JIRA does not modify or store any data in this directory.
The directories/files described below are found under the different sub-directories of the JIRA Installation directory, depending on whether you have installed JIRA Standalone or JIRA EAR/WAR. Please substitute the following directories for the <install-dir> placeholder below, as follows:
atlassian-jira subdirectorywebapp subdirectory (please note, if you want to edit any files in the webapp directory you will need to copy them to the edit-webapp subdirectory and edit the copies as described in JIRA WAR-EAR Configuration Overview. Copies of the jira-application.properties and entityengine.xml file are already available in the edit-webapp sub-directory).WEB-INF/classes/jira-application.propertiesThis file tells JIRA where to find the JIRA Home Directory, as well as storing many other configuration settings . This file is modified by the administrator when installing JIRA Standalone (not using Windows installer) or Installing JIRA WAR-EAR.
WEB-INF/classes/osuser.xmlThis file is modified when connecting JIRA to an external user management system such as an LDAP server or Atlassian's Crowd. For more information, refer to User and Group Management.
WEB-INF/lib/This is the directory where plugins built on Atlassian's Plugin Framework 1 (i.e. 'Plugins 1' plugins) are stored. If you are installing a new 'Plugins 1' plugin, you will need to deploy it into this directory.
 'Plugins 2' plugins should be stored in the JIRA Home directory.
WEB-INF/classes/log4j.propertiesJIRA のログ構成ファイルです。Logging and Profiling。
Jira によって生成された実際のログファイルは、次の場所で確認できます。
bin/atlassian-jira.loglogs directory. However, this can vary depending on the application server you are running. Please see Where are the application server logs? for further details.WEB-INF/classes/entityengine.xmlこのファイルは、JIRA が永続的データをデータソース内に保存する際に利用する、OFBiz エンティティエンジンを構成します。Configuring the Entity Engine for JIRA。
以下に解説するサブディレクトリ/ファイルは、JIRA インストレーションディレクトリのルートに存在します。
conf/server.xmlこのファイルは、JIRA SSL 構成に利用します。JIRA を SSL または HTTPS 上で実行する。
JAVA_OPTS メモリ設定の編集に使用されるファイルは、Jira のインストール方法、およびインストールに使用されたオペレーティング システムによって異なります。
For example, if you are running JIRA on Tomcat in Windows (manual startup), you would update the following file:
 bin\setenv.bat
 whereas for JIRA on Tomcat in Unix, you would update this file:
 bin/setenv.sh
詳しくは Increasing JIRA Memory を参照して下さい。