As the title of this section states, this relates to the early days of SharePoint, between SharePoint Portal Server 2001 and SharePoint Portal Server 2003. These two versions did not have a way to formally package, deploy, or retract custom code. Developers resorted to all kinds of hacks and kludges that kind of work, but did not really respect any solid development approaches, such as application lifecycle management or version control.
Developers would simply open a remote connection (typically via Remote Desktop) to a SharePoint 2001/2003 server, find the file they needed to modify, and use either Notepad on the server or copy the file for additional editing on their own workstation. Files would reside in the SharePoint Hive, under such directories as C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\<version>\. Each SharePoint server, if you had several in a farm configuration, would have identical files. Thus, changing one file on a single server would require you to change the same file identically on other servers as well.
In a way, this was a quick, fast, and reasonably well-understood approach. If you needed a change within SharePoint, you could simply figure out which file was responsible for the change and inject your changes to that file only. The result would often be so-so and kind of acceptable--until the next Service Pack was released and installed on the very same SharePoint server. At best, it would simply wipe customizations and force you to re-do all your changes once more. At worst, it would break something horribly as some files would now be patched with the Service Pack's version, while others would be customized and there would be no knowing what had gone wrong and where. Pages wouldn't load and random errors would occur for users.
One inventive, although certainly unsupported approach, was to tinker with Windows' Internet Information Services (IIS) web server settings to fool SharePoint just a tiny bit. SharePoint typically, at the time, mapped the infamous /_layouts/ virtual directory to the SharePoint Hive under C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\<version>\ subdirectories. Clever system administrators and developers would copy the hive directory structure to a sibling directory structure, and map the virtual directory from /_layouts/ in IIS to this new copy of the original files. In practical terms, this allowed one to tinker with the files without fear that original files would be destroyed. Upon new Service Pack deployments, you could point the virtual directory back to the original hive, allow patching to complete, and then do a file diff comparison between the original (patched) hive and your customized hive. Talk about spending a lot of time to get to your results!
Luckily, SharePoint versions 2001 and 2003 are not supported and we haven't seen these versions in production in years. But this is where it all started back in the day.