The italicized paragraphs at the top of some sections are information about whether the section contains spoilers for the version you're reading. Here you can find more in-depth explanations of them.
If a section has no warning, it means that you don't need to have any fear of being spoiled.
"This section applies to the IALCOTN."
This means that the section is made for readers of the IALCOTN (the newest version); it will not discuss any plot points that have not yet been mentioned in the IALCOTN, will be updated as the IALCOTN progresses, and is designed to go with it more than older versions.
"This section applies to the ILCOE."
This means that the section discusses the 3.x versions of the fic - the HMMRCIG, the YAR, the ILCOE and the ILCOTEM. Only those who have read all the chapters of the ILCOE are advised to read those sections.
"This section may contain spoilers for all versions of the fic."
This means that something in that section will be in the future of the story, but no version of the fic has ever gotten to that point. The information will of course be very minor and will not exactly spoil the fic for anybody.