Update changelogs, update deps, update docs and mdbook

Author: Polleps

CHANGELOG.md

@@ -7,6 +7,7 @@ See [STATUS.md](server/STATUS.md) to learn more about which features will remain
 
 ## UNRELEASED
 
+- We changed the binary format in which resources are stored. This means your data will be migrated the first time you run the server. This could take some time depending on the size of your database.
 - [#1048](https://github.com/atomicdata-dev/atomic-server/issues/1048) Fix search index not removing old versions of resources.
 - [#1056](https://github.com/atomicdata-dev/atomic-server/issues/1056) Switched from Earthly to Dagger for CI. Also made improvements to E2E test publishing and building docker images.
 - [#979](https://github.com/atomicdata-dev/atomic-server/issues/979) Fix nested resource deletion, use transactions
@@ -16,8 +17,9 @@ See [STATUS.md](server/STATUS.md) to learn more about which features will remain
 - [#958](https://github.com/atomicdata-dev/atomic-server/issues/958) Fix search in CLI / atomic_lib
 - [#658](https://github.com/atomicdata-dev/atomic-server/issues/658) Added JSON datatype.
 - [#1024](https://github.com/atomicdata-dev/atomic-server/issues/1024) Added URI datatype.
+- [#998](https://github.com/atomicdata-dev/atomic-server/issues/998) Added YJS datatype.
 BREAKING: [#1107](https://github.com/atomicdata-dev/atomic-server/issues/1107) Named nested resources are no longer supported. Value::Resource and SubResource::Resource have been removed. If you need to include multiple resources in a response use an array.
-BREAKING: `store.get_resource_extended()` now returns a `ResourceResponse` instead of a `Resource` due to the removal of named nested resources.
+BREAKING: `store.get_resource_extended()` now returns a `ResourceResponse` instead of a `Resource` due to the removal of named nested resources. Use `.into()` or `.to_single()` to convert to a `Resource`.
 
 ## [v0.40.2]
 

browser/CHANGELOG.md

@@ -6,6 +6,10 @@ This changelog covers all five packages, as they are (for now) updated as a whol
 
 ### Atomic Browser
 
+- [#741](https://github.com/atomicdata-dev/atomic-server/issues/741) New feature: A brand new document editor with realtime collaboration and a fast and efficient editing experience.
+- [#951](https://github.com/atomicdata-dev/atomic-server/issues/951) New feature: Atomic Assistant, AI chat interface with support for custom agents, MCP servers and more. Bring your own OpenRouter key or use Ollama to host your own models.
+- [#459](https://github.com/atomicdata-dev/atomic-server/issues/459) New feature: Add tags to your resources to better organize your data. Search for resources with specific tags in the search bar with `tag:[name]`.
+- [#1118](https://github.com/atomicdata-dev/atomic-server/issues/1118) New feature: AtomicServer is now also available in German, Spanish and French. Change your language on the settings page.
 - [#981](https://github.com/atomicdata-dev/atomic-server/issues/981) Fix bug where the service worker would not update cache with updated code.
 - [#989](https://github.com/atomicdata-dev/atomic-server/issues/989) Added an edit button to the resource selector inputs.
 - [#992](https://github.com/atomicdata-dev/atomic-server/issues/992) Fix Searchbox overflowing when displaying long names.
@@ -17,9 +21,6 @@ This changelog covers all five packages, as they are (for now) updated as a whol
 - [#1008](https://github.com/atomicdata-dev/atomic-server/issues/1008) Add 'open' option to classes and properties in the ontology edit view.
 - [#1008](https://github.com/atomicdata-dev/atomic-server/issues/1008) Updated the look of the resource selector and made it more responsive.
 - [#1008](https://github.com/atomicdata-dev/atomic-server/issues/1008) Add info dropdowns to different sections of the ontology editor for more information about the section.
-- [#459](https://github.com/atomicdata-dev/atomic-server/issues/459) New feature: Add tags to your resources to better organize your data. Search for resources with specific tags in the search bar with `tag:[name]`.
-- [#951](https://github.com/atomicdata-dev/atomic-server/issues/951) New feature: Atomic Assistant, AI chat interface with support for custom agents, MCP servers and more. Bring your own OpenRouter key or use Ollama to host your own models.
-- [#1118](https://github.com/atomicdata-dev/atomic-server/issues/1118) New feature: AtomicServer is now also available in German, Spanish and French. Change your language on the settings page.
 
 ### @tomic/lib
 
@@ -32,7 +33,7 @@ This changelog covers all five packages, as they are (for now) updated as a whol
 - Added `ResourceEvents.LoadingChange` event on `Resource` to listen for changes to the loading state of the resource.
 - Added `resource.stable` property to `Resource` to get a stable reference to the resource, even when it is proxied.
 - Added `resource.merge()` method to merge a resource into another resource while preserving local changes on the current resource.
-- `store.addResources()` now merges incoming resources with resources already present in the store.
+- `store.addResources()` now merges incoming resources with resources already present in the store instead of replacing them.
 - SEMI BREAKING CHANGE: When using generated types by cli, @tomic/lib now requires them to be generated by @tomic/cli v0.41.0 or above.
 - BREAKING CHANGE: The `StoreEvents.ResourceRemoved` event callback now only receives the subject of the resource instead of the resource itself.
 

browser/README.md

@@ -38,7 +38,7 @@ pnpm start # run the server!
 
 Library with `Store`, `Commit`, `JSON-AD` parsing, and more.
 
-[**docs**](https://atomic-lib.netlify.app/modules/_tomic_lib)
+[**docs**](https://docs.atomicdata.dev/js.html)
 
 [→ Read more](lib/README.md)
 
@@ -59,7 +59,7 @@ React library with many useful hooks for rendering and editing Atomic Data.
 
 [**demo + template on codesandbox**](https://codesandbox.io/s/atomic-data-react-template-4y9qu?file=/src/MyResource.tsx:0-1223)
 
-[**docs**](https://atomic-lib.netlify.app/modules/_tomic_react)
+[**docs**](https://docs.atomicdata.dev/usecases/react.html)
 
 [→ Read more](react/README.md)
 

browser/data-browser/package.json

@@ -18,7 +18,7 @@
     "@emoji-mart/react": "^1.1.1",
     "@emotion/is-prop-valid": "^1.4.0",
     "@floating-ui/dom": "^1.7.4",
-    "@modelcontextprotocol/sdk": "^1.22.0",
+    "@modelcontextprotocol/sdk": "^1.23.0",
     "@oddbird/css-anchor-positioning": "^0.6.1",
     "@openrouter/ai-sdk-provider": "^1.2.5",
     "@radix-ui/react-popover": "^1.1.15",

browser/package.json

@@ -13,7 +13,7 @@
     "eslint-plugin-react-hooks": "7.0.1",
     "globals": "^15.11.0",
     "husky": "^8.0.3",
-    "netlify-cli": "17.37.1",
+    "netlify-cli": "23.11.1",
     "prettier": "3.6.2",
     "prettier-plugin-jsdoc": "^1.3.0",
     "prettier-plugin-svelte": "^3.2.7",