How effective are tools such as w3af in looking for web app vulnerabilities compared to looking for vulnerabilities manually? Are they able to find all vulnerabilities from OWASP top 10 such as reflected xss, persistent xss, sqli, lfi/rfi, and unrestricted file upload? Or will some vulnerabilities fall through the cracks and remain undiscovered?
W3af vs manual penetration testing
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You cannot possibliy find all the vulnerabilities through one method --manual or auto--, it is the halting problem. An automated method will consistently find some, but will surely lack coverage, may produce false positive alarms and will also fail to investigate a potential vulnerability with sufficent depth to uncover it. A manual procedure, can be better or worse, depending on the skills of the tester and how much resources he invests.