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You are right, in part...
In the second episode of the first season Rory awakes her mother and she goes from her bedroom to the bathroom...
And aparently there it's nothing more in that floor...
Something completely absurd seeing the "theoretical" exterior of the building...
The entire first floor of the home is built to scale in a studio but the first floorplan sceens were filmed in removable sets.
In the place wher I placed the bathroom of the ground flour there was nothing, only a hallway to comunicate withe the backside of the soundstage.
But mi idea was make this floorplan as "real houses", not as studio sets.
So I prefer to draw a bathroom here instead an empty space to... nowhere.
My logic says that this house deserves a bathroom in the ground floor to Rory and the guest.
The bathroom of the first floor is not enough.
Especially when in theory disappears after the makeover and the common bathroom is now an ensuite bathroom.
Do you will purchase a house with only an ensuite bathroom and nothing in the ground floor ???
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When Lorelai's bedroom appears for the first time in the episode 1X02 apparently the first fllorplan only contains her bedroom at one side (above the living room) and a bathroom in the other side.
But, what happens with all the rest of the space in this floor above kitchen and Rory's bedroom ???
In fact an image of the other side of the fake building was shown to situate the action in Lorelai's bedroom:
[link]
But this side of the building creates contradictions with the distribution of the sets.
In fact this image situates the bedroom in the backside but in the episode 6.02 we can see Lorelai's bedroom in a travelling through a big hole in the wall.
So the windows in Lorelai's bedroom are placed looking to this side of the house.
Three windows in a flat wall, another contradiction.
[link]
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In the epissode 6.06 we attend to the makeover and in the next episodes the new bedroom is presented.
In theory this new bedroom is situated in the same place as the old one but the access to this new bedroom it's through a long corridor wich creates another contradiction with the situation of the stairs.
So finally I decided to make my own theory:
The old bedroom was reconstructed and used now as guest bedroom. The new bedroom was created in the unused space above kitchen and Rory's bedroom extending the original bathroom on upper floor to create the ensuite bathroom.
I adapted the stairs to fit the old bedroom with the ground floor and to create a long corridor to the new bedroom.
I don't know why (maybe cause all these changes creates confussion) but the producers never shows the upper part of the exterior of the house in the rest of episodes.
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They was an easiest option to my:
I can make a floorplan of the upper floor with only the bedroom from the first episodes.
But many fans will say: What is happens with the new bedroom of the final episodes ???
And I can make a floorplan of the upper floor with only the new bedroom from the last episodes.
But many fans will say: What happens with the old bedroom ???
And also I can draw an empty space where the bathroom of the ground floor was placed, but the house will be... incomplete.

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Hello.
Thank you very much...
Seeing pictures of the exterior of the house they are visible some windows in the lower part so (theorically) the house has a basement...
[link]
It was impossible to fit an access to this basement inside the house
So I placed the entrance to the basement from the rear side of the house and fit the proportions of the distribution with the entry dor and veranda of the kitchen...
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