The line-by-line code review is self explanatory – it involves reading all the source code. Unfortunately, a line-by-line review is unlikely to immediately lead to discovering all the issues in the code (in fact there are better ways to systemically go through all the code when incorporating the specification).
The goals of line-by-line review, especially when conducted early in the process are the following:
A good tool to use for line-by-line review is the Solidity Visual Developer. It offers security-aware syntax highlighting and other visualization tools.