For example, if you have completed Mena's and Lucy's routes and have begun to work on Kitty's, you are starting your third run.
New choices become available in later runs, and are noted as such in the walkthrough.
Equipment
Equipment is noted in the walkthrough with black and bold font.
Unlike items, equipment does not respawn in future runs (meaning you cannot have more than one piece of the same equipment).
Gold (also known as Zel) will spawn in place of the equipment you have already picked up.
The "+" Sign
Placed at the end of a line means "and thereafter" (for example "Run 2+" means that it must be at least your second run).
Placed at the beginning of a line means "in addition to" (for example "Pumpkin's Forest Mission + All Ghost-Related Events" means that both of those conditions must be met for the event to occur).
"Affectionate [Character]"
An "affectionate" character is someone who you have spent enough time with (usually during your free time at nights) to raise her flag for a specific event.
To make someone affectionate, simply visit the person at nights (or perhaps wherever she is during the day) until the event is activated.
Miscellaneous
You must complete Mena's and Lucy's routes before having access to Kitty's and Aoi's.
Sheryl's route only becomes available after completing the other four (Mena's, Lucy's, Kitty's, and Aoi's).
It is impossible to get all of Mena's CGs in your first run with her. To get the final CGs, you must aim for Kitty's path up until when the walkthrough asks you to save, and then proceed down Mena's path (after already completing Mena's path once).
The order of some events are not set in stone. For example, it is possible to receive the emergency fund from Iry before receiving the mission from the Mayor.