A Web Application Scanner Tool Functional Specification is available.
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Web Applications Issues
- Scripting issues
 - Sources of input: forms, text boxes, dialog windows, etc.
 - Multiple Charset Encodings (UTF-8, ISO-8859-15, UTF-7, etc.)
 - Regular expression checks
 - Header integrity (e.g. Multiple HTTP Content Length, HTTP Response Splitting)
 - Session handling/fixation
 - Cookies
 - Framework vulnerabilities(Java Server Pages, .NET, Ruby On Rails, Django, etc.)
 - Success control: front door, back door vulnerability assessment
 - Penetration attempts versus failures
 
Technical vulnerabilities
- Unvalidated input: 
- Tainted parameters - Parameters users in URLs, HTTP headers, and forms are often used to control and validate access to sentitive information.
 - Tainted data
 
 - Cross-Site Scripting flaws: 
- XSS takes advantage of a vulnerable web site to attack clients who visit that web site. The most frequent goal is to steal the credentials of users who visit the site.
 
 - Content Injection flaws: 
- Data injection
 - SQL injection - SQL injection allows commands to be executed directly against the database, allowing disclosure and modification of data in the database
 - XPath injection - XPath injection allows attacker to manipulate the data in the XML database
 - Command injection - OS and platform commands can often be used to give attackers access to data and escalate privileges on backend servers.
 - Process injection
 
 - Cross-site Request Forgeries
 
Security Vulnerabilities
- Denial of Service
 - Broken access control
 - Path manipulation
 - Broken session management (synchronization timing problems)
 - Weak cryptographic functions, Non salt hash
 
Architectural/Logical Vulnerabilities
- Information leakage
 - Insufficient authentification
 - Password change form disclosing detailed errors
 - Session-idle deconstruction not consistent with policies
 - Spend deposit before deposit funds are validated
 
Other vulnerabilities
- Debug mode
 - Thread Safety
 - Hidden Form Field Manipulation
 - Weak Session Cookies: Cookies are often used to transit sensitive credentials, and are often easily modified to escalate access or assume another user's identify.
 - Fail Open Authentication
 - Dangers of HTML Comments
 
Related Links
- The Web Application Security Consortium (WASC) has a list of web application security scanners.
 - The Open Web Application Security Project (OWASP) Phoenix has a list of various web application testing tools.
 - Shay Chen's article has a list of test cases for web application scanners.