diff --git a/README.md b/README.md
index 39881e9..d467f53 100644
--- a/README.md
+++ b/README.md
@@ -16,11 +16,11 @@ Welcome to the Internet of Peers
 
 References for utilizing the Pear runtime.
 
-* [Command-Line-Interface (CLI)](./reference/cli.md)
-* [Application-Programming-Interface (API)](./reference/api.md)
-* [Application Configuration](./reference/configuration.md)
+* [Command-Line-Interface (CLI)](./reference/pear/cli.md)
+* [Application-Programming-Interface (API)](./reference/pear/api.md)
+* [Application Configuration](./reference/pear/configuration.md)
 
-> The Pear runtime uses [Bare](https://github.com/holepunchto/bare) JavaScript runtime, which is a small and modular JavaScript runtime for desktop and mobile. To learn more, see [Bare Reference](./bare-reference/overview.md).
+> The Pear runtime uses [Bare](https://github.com/holepunchto/bare) JavaScript runtime, which is a small and modular JavaScript runtime for desktop and mobile. To learn more, see [Bare Reference](./reference/bare/overview.md).
 
 ### Guides
 
diff --git a/SUMMARY.md b/SUMMARY.md
index 0d4901d..ca55578 100644
--- a/SUMMARY.md
+++ b/SUMMARY.md
@@ -4,15 +4,15 @@
 
 ### Pear runtime
 
-* [Command-Line-Interface (CLI)](./reference/cli.md)
-* [Application-Programming-Interface (API)](./reference/api.md)
-* [Application Configuration](./reference/configuration.md)
+* [Command-Line-Interface (CLI)](./reference/pear/cli.md)
+* [Application-Programming-Interface (API)](./reference/pear/api.md)
+* [Application Configuration](./reference/pear/configuration.md)
 
 ### Bare reference
-* [Overview](./bare-reference/overview.md)
-* [Application-Programming-Interface (API)](./bare-reference/api.md)
-* [Node.js Compatibility with Bare](./bare-reference/nodejs-compatibility-with-bare.md)
-* [Bare Modules](./bare-reference/bare-modules.md)
+* [Overview](./reference/bare/overview.md)
+* [Application-Programming-Interface (API)](./reference/bare/api.md)
+* [Node.js Compatibility with Bare](./reference/bare/nodejs-compatibility-with-bare.md)
+* [Bare Modules](./reference/bare/bare-modules.md)
 
 ### Guides
 
diff --git a/guide/making-a-pear-desktop-app.md b/guide/making-a-pear-desktop-app.md
index 2692bd4..55f5a0f 100644
--- a/guide/making-a-pear-desktop-app.md
+++ b/guide/making-a-pear-desktop-app.md
@@ -262,7 +262,7 @@ function onMessageAdded (from, message) {
 }
 ```
 
-> Note that the `pear` dependency is used, even though it was not installed. This is the [Pear API](../reference/api.md), available to any Pear project.
+> Note that the `pear` dependency is used, even though it was not installed. This is the [Pear API](../reference/pear/api.md), available to any Pear project.
 
 
 ## Step 4. Chat
diff --git a/guide/starting-a-pear-desktop-project.md b/guide/starting-a-pear-desktop-project.md
index 36b49db..e254862 100644
--- a/guide/starting-a-pear-desktop-project.md
+++ b/guide/starting-a-pear-desktop-project.md
@@ -45,7 +45,7 @@ The app should now show:
 
 ![Automatic reload](../assets/chat-app-2.png)
 
-> Live reload with hot-module reloading is possible by using the `pear.watch` configuration and the [`pear.updates`](../reference/api.md#pearupdateslistener-async-functionfunction) API. The [pear-hotmods](https://github.com/holepunchto/pear-hotmods) convenience module can also be used.
+> Live reload with hot-module reloading is possible by using the `pear.watch` configuration and the [`pear.updates`](../reference/pear/api.md#pearupdateslistener-async-functionfunction) API. The [pear-hotmods](https://github.com/holepunchto/pear-hotmods) convenience module can also be used.
 
 ## Step 4. Configuration
 
@@ -69,7 +69,7 @@ Open `package.json` and update it to:
 
 Close the app and re-run `pear dev` to see the changes:  the background is now light blue, and the initial window size is different.
 
-See the [Configuration Documentation](../reference/configuration.md) for all options.
+See the [Configuration Documentation](../reference/pear/configuration.md) for all options.
 
 
 ## Next
diff --git a/bare-reference/api.md b/reference/bare/api.md
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diff --git a/bare-reference/bare-modules.md b/reference/bare/bare-modules.md
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rename from bare-reference/bare-modules.md
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diff --git a/bare-reference/nodejs-compatibility-with-bare.md b/reference/bare/nodejs-compatibility-with-bare.md
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rename from bare-reference/nodejs-compatibility-with-bare.md
rename to reference/bare/nodejs-compatibility-with-bare.md
diff --git a/bare-reference/overview.md b/reference/bare/overview.md
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diff --git a/reference/api.md b/reference/pear/api.md
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diff --git a/reference/configuration.md b/reference/pear/configuration.md
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