Sometimes when a Godot project loads, it cannot find classes or references

I'm developing an open source level editor (https://github.com/blackears/cyclopsLevelBuilder) and keep running into a problem when I make a small change and then everything breaks. Or I revert my project after making a bad change and nothing works because Godot is no longer able to resolve class names or resource paths properly. Identical code that was working perfectly well one session starts spewing a ton of errors about class name collisions or resources that are clearly there but are now returning Nil when loaded. For example:
res://addons/cyclops_level_builder/resources/tool_tag.gd:36 - Parse Error: Could not parse global class "CyclopsLevelBuilder" from "res://addons_disabled/cyclops_level_builder/cyclops_level_builder.gd".
res://addons/cyclops_level_builder/tools/tool_move.gd:26 - Parse Error: Class "ToolMove" hides a global script class.
res://addons/cyclops_level_builder/tools/tool_move.gd:0 - Parse Error: Could not resolve class "CyclopsTool".
res://addons/cyclops_level_builder/tools/tool_move.gd:44 - Parse Error: Could not parse global class "CommandMoveBlocks" from "res://addons_disabled/cyclops_level_builder/commands/cmd_move_blocks.gd".
res://addons/cyclops_level_builder/tools/tool_move.gd:233 - Parse Error: Could not parse global class "CyclopsLevelBuilder" from "res://addons_disabled/cyclops_level_builder/cyclops_level_builder.gd".

I also tried checking this project out on my macbook recently and was getting a lot of errors that resources could not be found, even though they're in the resource directory and the project was working well on my development machine.

What's most infurating is that identical code can run just fine in one project can throw a ton of errors about missing resources and name collisions in another project. Is there any way to get the editor to clear out whatever it has cached and build the project new?