: Are there tools/software for planning your story using nested mindmaps and references to characters? I've been looking for a certain piece of software for a long time, but I never quite found

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Any decent mind mapping software would do.
We commonly use editors for words, sheets, and slides, but there do exist editors for mind maps. As a class of software. Desktop and online.
Almost all of them support what you asked for.

I personally use Mindjet Mind Manager (ten years old verion, but still 200% functions to cover all my requirements):

nested mind maps, including links to other files;
easy references, tags, visual stuff, etc

Export to Word is a powerfull feature.

I easily wrote and edited a complex draft using a visual tree of logical blocks (chapters, paragraphs), with notes attached to each block. Then exported the entire story into Word.
In visual mode I had a logical structure with to dos, completion progress, research notes and even alternative branches. I edited notes, marked the ones I liked as "completed", and clicked "Export".
Once exported, it was a clean text in Word with styles I pre-configured.
A clean, proofread, logically structured, and formatted book in MS Word from a pile of notes with a click!

It is a paid software, but there are similar apps for free as well, I believe.

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World Anvil
www.worldanvil.com/about
I like using this website for world building/story creation because there is so much available and it can all be interconnected. Though you can't see all these things in detail at once, they're there visually in the sidebar.

You can link characters to other characters
You can link characters to articles
You can make timelines
You can make complex relationships between characters
You can make notes and secrets that aren't in the main profile for whatever it is you're making (e.g. a character).

The one thing I don't know for sure is if you can find and replace one word. I haven't used it all that much the way it's designed to work because I don't want to subscribe.

I made a few random characters, places, governments, organizations, etc. for you to see how it works. Here's the link. Note that I didn't fill out all the areas just because there are SO MANY. If you're interested I suggest you make a free account, make a world and poke around.

Here's a link to someone else's public, much more well done character. PLEASE, look around their world, it's much better than the one I threw up and shows you more of what yours might look like. In the articles they've written, you can see that when another character is references, they have chosen to put a link to that character's profile. (Their character is for game play not writing, so it has powers and levels, etc.)

The downsides

You have to subscribe if you want your world(s) to be private
If you don't have an ad blocker there are adds on the side.

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archivos.digital/about-archivos/ ARCHIVOS sounds like what you need.
(I saw a demo about it at BaltiCon last year, and it's in my pocket as something to explore when I have brain-space for it.)
From their about page:

First, ARCHIVOS helps Storytellers document the characters, places, and events of their stories, detailing the basic framework for the tale.
Then, Storytellers connect those story elements by defining the relationships between them that articulate not just the existence of the connection but also its nature (professional, personal, political, geographical, etc.).
The relationships in ARCHIVOS also support a hierarchy, like that of a parent to a child, or a manager to an employee. This framework will help identify and organize the structures within the story world.

In their FAQs, they appear to describe these changes you want:

Your element roster is displayed with additional details, all of it sortable and searchable. But the best part is the ability to select multiple elements and apply an update to all of them. Quickly save or hide or show dozens of elements with the click of a mouse.

It's free for the basic level, which I think allows unlimited elements within a single "story world"
Let me know if this meets your needs!

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All software is limited by
a. what the software creator allows you to do with it, and
b. screen real estate.
Like you I am a person who needs to organize their notes both visually and spacially. Having information off screen – either in parts of the current file that lie outside the viewing area because I have zoomed in or in other windows behind the current one or even in other files in other software – makes organizing my mind impossible for me. And being unable to draw lines and order the content of a file whichever way I want makes all software that I have reviewed a severe hindrance in creative thinking.
The most flexible and versatile tool that I have found for me is
pen and paper
Many of my notes and ideas are handwritten in notebooks or on small slips of paper, others I have on a computer and print out and cut into sections with scissors. I then sit on the floor and play with these snippets until they are in the order I want them to be. Sometimes I glue some pieces together, or number them, or whatever I want.
Here is an image (from some group effort at brainstorming, but it shows what I mean):

Other people like to combine a whiteboard and post-it:

You can take a photo, if you want to preserve a certain state of the process. What I do is order my notes into a special binder (in German it is called Vorordner):

There are "pockets", often either numbered or labelled alphabetibally, into which I put the notes for chapters (one pocket = one chapter), characters (one pocket = one character), or steps (in a screenplay). That way they stay organized. I can take out the notes for one section, add to them or reorganize them elsewhere. When I'm done planning, I begin to write from these notes, one pocket at a time, or work the relevant information into another format, either on paper or in an electronic file.

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I use a program called yWriter6. It is developed by an author, Simon Haynes (who also happened to be a terrific programmer) and tailored to most writing needs. It can be downloaded for free.

What it does best to save your work in scenes with each having enough note for further world-building or plotting, which can be easily referred no matter where you are in the story. These scenes can be nested within chapters or moved around, and are easily referenced.

Similarly, there are also segments for characters where you could flesh out details. Changes to them can be easily made to reflect on the work itself. Each chapter has a list of characters making appearance in it as a side note.

Besides this, there are word count target prompts, segments for locations and key items, a storyboard page, spaces to mark story goals, conflict, and outcome.

Still new to stackexchange, so not certain if I'm permitted to share links to works here. But goggle yWriter or Simon Haynes and you'd be able to find it.

EDIT: link to Ywriter.

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I have two recommendation, but neither only fully meets your criteria:

There is Scrivener. It is a full text editor made for writer. It has elaborate note taking features for characters, locations, etc. I believe it meets your criteria for integration, but it is not visual. You can quickly reference your notes, but it doesn't have the automatic update feature you are interested in (I don't know of anything that does.) You can find it here.
What I use for more note taking (since I also like to visual things) is Scapple. It is from the same developers of Scrivener. It is entirely visual based, nested, and has search features. However, you don't write your book directly in Scapple, so there is no character reference ability. I love it. You can find it here.

So, what do I recommend? Both. I use and love both. Scapple for visual note taking and Scrivener for writing/text notes.

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