diff --git a/docs/docs/_partial-export-flows.mdx b/docs/docs/_partial-export-flows.mdx
new file mode 100644
index 00000000..bbab64e6
--- /dev/null
+++ b/docs/docs/_partial-export-flows.mdx
@@ -0,0 +1 @@
+1. If you modified the built-in flows or created custom flows in your [OpenRAG Langflow instance](/agents), and you want to preserve those changes, then you must [export your flows](https://docs.langflow.org/concepts-flows-import) before starting this process. Afterwards, you can import your flows or reference the exported flow JSON as needed.
\ No newline at end of file
diff --git a/docs/docs/_partial-factory-reset-warning.mdx b/docs/docs/_partial-factory-reset-warning.mdx
index 97f2ca7e..c1e11894 100644
--- a/docs/docs/_partial-factory-reset-warning.mdx
+++ b/docs/docs/_partial-factory-reset-warning.mdx
@@ -1,14 +1,11 @@
 :::warning
-This is a destructive action that does the following:
+This is a destructive operation that does the following:
 
-* Destroys all OpenRAG containers, volumes, and local images with `docker compose down --volumes --remove-orphans --rmi local`.
-* Prunes any additional container objects with `docker system prune -f`.
-* Deletes the contents of OpenRAG's `config` and `./opensearch-data` directories.
-* Deletes the `conversations.json` file.
+* Destroys all OpenRAG containers, volumes, and local images.
+* Prunes any additional container objects.
+* Deletes the contents of the `~/.openrag` directory _except_ for OpenRAG's `.env` file and the `/documents` subdirectory.
 
 <p/>Destroyed containers and deleted data are lost and cannot be recovered after running this operation.
-
-This operation _doesn't_ remove the `.env` file or the contents of the `./openrag-documents` directory.
 :::
 
 <!--
diff --git a/docs/docs/_partial-setup.mdx b/docs/docs/_partial-setup.mdx
index 9af2ecbf..8142844d 100644
--- a/docs/docs/_partial-setup.mdx
+++ b/docs/docs/_partial-setup.mdx
@@ -37,7 +37,7 @@ If OpenRAG detects OAuth credentials during setup, it recommends **Advanced Setu
 
 4. Click **Save Configuration**.
 
-   Your passwords and API key, if provided, are stored in the [OpenRAG `.env` file](/reference/configuration) in your OpenRAG installation directory.
+   Your passwords and API key, if provided, are stored in the [OpenRAG `.env` file](/reference/configuration) at `~/.openrag/tui`.
    If you modified any credentials that were pulled from an existing `.env` file, those values are updated in the `.env` file.
 
 5. Click **Start All Services** to start the OpenRAG services that run in containers.
@@ -81,7 +81,7 @@ If OpenRAG detects OAuth credentials during setup, it recommends **Advanced Setu
    If you aren't sure which models or providers to use, you must provide an OpenAI API key to use OpenRAG's default model configuration.
    If you want to use a different model provider, you can leave this field empty.
 
-4. To upload documents from external storage, such as Google Drive, add the required OAuth credentials for the connectors that you want to use. These settings can be populated automatically if OpenRAG detects these credentials in an [OpenRAG `.env` file](/reference/configuration) in the OpenRAG installation directory.
+4. To upload documents from external storage, such as Google Drive, add the required OAuth credentials for the connectors that you want to use. These settings can be populated automatically if OpenRAG detects these credentials in an [OpenRAG `.env` file](/reference/configuration) at `~/.openrag/tui`.
 
    * **Amazon**: Provide your AWS Access Key ID and AWS Secret Access Key with access to your S3 instance. For more information, see the AWS documentation on [Configuring access to AWS applications](https://docs.aws.amazon.com/singlesignon/latest/userguide/manage-your-applications.html).
    * **Google**: Provide your Google OAuth Client ID and Google OAuth Client Secret. You can generate these in the [Google Cloud Console](https://console.cloud.google.com/apis/credentials). For more information, see the [Google OAuth client documentation](https://developers.google.com/identity/protocols/oauth2).
@@ -95,7 +95,7 @@ Register these redirect values with your OAuth provider as they are presented in
 
 6. Click **Save Configuration**.
 
-   Your passwords, API key, and OAuth credentials, if provided, are stored in the [OpenRAG `.env` file](/reference/configuration) in your OpenRAG installation directory.
+   Your passwords, API key, and OAuth credentials, if provided, are stored in the [OpenRAG `.env` file](/reference/configuration) at `~/.openrag/tui`.
    If you modified any credentials that were pulled from an existing `.env` file, those values are updated in the `.env` file.
 
 7. Click **Start All Services** to start the OpenRAG services that run in containers.
diff --git a/docs/docs/core-components/agents.mdx b/docs/docs/core-components/agents.mdx
index d242552d..32387a59 100644
--- a/docs/docs/core-components/agents.mdx
+++ b/docs/docs/core-components/agents.mdx
@@ -32,7 +32,7 @@ For example, to view and edit the built-in **Chat** flow (the **OpenRAG OpenSear
 
    If prompted to acknowledge that you are entering Langflow, click **Proceed**.
 
-   If Langflow requests login information, enter the `LANGFLOW_SUPERUSER` and `LANGFLOW_SUPERUSER_PASSWORD` from your [OpenRAG `.env` file](/reference/configuration) in your OpenRAG installation directory.
+   If Langflow requests login information, enter the `LANGFLOW_SUPERUSER` and `LANGFLOW_SUPERUSER_PASSWORD` from your [OpenRAG `.env` file](/reference/configuration).
 
    ![OpenRAG OpenSearch Agent flow](/img/opensearch-agent-flow.png)
 
@@ -59,6 +59,12 @@ In addition to OpenRAG's built-in flows, all Langflow features are available thr
 
 Explore the [Langflow documentation](https://docs.langflow.org/) to learn more about the Langflow platform, features, and visual editor.
 
+## Modify a flow at runtime {#modify-a-flow-at-runtime}
+
+You can use _tweaks_ to modify flow settings at runtime without permanently changing the flow's configuration.
+Tweaks are one-time parameter modifications that are passed to specific Langflow components during flow execution.
+For more information on tweaks, see the Langflow documentation on [Input schema (tweaks)](https://docs.langflow.org/concepts-publish#input-schema).
+
 ## Set the Langflow version
 
 By default, OpenRAG is pinned to the latest Langflow Docker image for stability.
diff --git a/docs/docs/core-components/ingestion.mdx b/docs/docs/core-components/ingestion.mdx
index 7a69e3dd..f584405e 100644
--- a/docs/docs/core-components/ingestion.mdx
+++ b/docs/docs/core-components/ingestion.mdx
@@ -32,7 +32,7 @@ You can upload files and folders from your local machine to your knowledge base:
 
 3. To upload one file, click <Icon name="File" aria-hidden="true"/> **File**. To upload all documents in a folder, click <Icon name="Folder" aria-hidden="true"/> **Folder**.
 
-   The default path is the `./documents` subdirectory in your OpenRAG installation directory.
+   The default path is `~/.openrag/documents`.
    To change this path, see [Set the local documents path](/knowledge#set-the-local-documents-path).
 
 The selected files are processed in the background through the **OpenSearch Ingestion** flow.
diff --git a/docs/docs/core-components/knowledge.mdx b/docs/docs/core-components/knowledge.mdx
index 31c6d8a1..c478a95a 100644
--- a/docs/docs/core-components/knowledge.mdx
+++ b/docs/docs/core-components/knowledge.mdx
@@ -137,14 +137,17 @@ The default value is 200 characters, which represents an overlap of 20 percent i
 
 ### Set the local documents path {#set-the-local-documents-path}
 
-The default path for local uploads is the `./openrag-documents` subdirectory in your OpenRAG installation directory. This is mounted to the `/app/openrag-documents/` directory inside the OpenRAG container. Files added to the host or container directory are visible in both locations.
+The default path for local uploads is `~/.openrag/documents`. This is mounted to the `/app/openrag-documents/` directory inside the OpenRAG container. Files added to the host or container directory are visible in both locations.
 
 To change this location, modify the **Documents Paths** variable in either the [**Advanced Setup** menu](/install#setup) or in your [OpenRAG `.env` file](/reference/configuration).
 
 ## Delete knowledge {#delete-knowledge}
 
-To clear your entire knowledge base, delete the contents of the `./opensearch-data` folder in your OpenRAG installation directory.
+:::warning
 This is a destructive operation that cannot be undone.
+:::
+
+To clear your entire knowledge base, [reset your OpenRAG containers](/manage-services#reset-containers) or [reinstall OpenRAG](/reinstall).
 
 ## See also
 
diff --git a/docs/docs/get-started/install-options.mdx b/docs/docs/get-started/install-options.mdx
index 90f800a5..eac24d46 100644
--- a/docs/docs/get-started/install-options.mdx
+++ b/docs/docs/get-started/install-options.mdx
@@ -27,8 +27,8 @@ This is required for all installation methods because it prepares the minimum re
 For TUI-managed services, you must also complete initial setup before you start the OpenRAG services.
 For more information, see the instructions for your preferred installation method.
 
-Your OpenRAG configuration is stored in a `.env` file in the OpenRAG installation directory.
-When using TUI-managed services, this file is created automatically, or you can provide a pre-populated `.env` file before starting the TUI.
+Your OpenRAG configuration is stored in a `.env` file.
+When using TUI-managed services, this file is created automatically at `~/.openrag/tui`, or you can provide a pre-populated `.env` file in this directory before starting the TUI.
 The TUI prompts you for the required values during setup and onboarding, and any values detected in a preexisting `.env` file are populated automatically.
 When using self-managed services, you must provide a pre-populated `.env` file, as you would for any Docker or Podman deployment.
 For more information, see the instructions for your preferred installation method and the [OpenRAG environment variables reference](/reference/configuration).
\ No newline at end of file
diff --git a/docs/docs/get-started/install-uv.mdx b/docs/docs/get-started/install-uv.mdx
index 9a73546e..bbd7f44c 100644
--- a/docs/docs/get-started/install-uv.mdx
+++ b/docs/docs/get-started/install-uv.mdx
@@ -80,7 +80,7 @@ If you encounter errors during installation, see [Troubleshoot OpenRAG](/support
 
    For more options, see [Managing dependencies with `uv`](https://docs.astral.sh/uv/concepts/projects/dependencies/).
 
-4. Optional: If you want to use a pre-populated [OpenRAG `.env` file](/reference/configuration), copy it to this directory before starting OpenRAG.
+4. Optional: If you want to use a pre-populated [OpenRAG `.env` file](/reference/configuration), create one at `~/.openrag/tui` before starting OpenRAG.
 
 5. Start the OpenRAG TUI:
 
@@ -98,7 +98,7 @@ If you encounter errors during installation, see [Troubleshoot OpenRAG](/support
    uv pip install openrag
    ```
 
-3. Optional: If you want to use a pre-populated [OpenRAG `.env` file](/reference/configuration), copy it to this directory before starting OpenRAG.
+3. Optional: If you want to use a pre-populated [OpenRAG `.env` file](/reference/configuration), create one at `~/.openrag/tui` before starting OpenRAG.
 
 4. Start the OpenRAG TUI:
 
@@ -111,7 +111,7 @@ If you encounter errors during installation, see [Troubleshoot OpenRAG](/support
 When you install OpenRAG with `uv`, you manage the OpenRAG services with the TUI.
 The TUI guides you through the initial configuration process before you start the OpenRAG services.
 
-Your configuration values are stored in an [OpenRAG `.env` file](/reference/configuration) that is created automatically in the Python project where you installed OpenRAG.
+Your configuration values are stored in an [OpenRAG `.env` file](/reference/configuration) that is created automatically at `~/.openrag/tui`.
 If OpenRAG detects an existing `.env` file in this directory, then the TUI can populate those values automatically during setup and onboarding.
 
 Container definitions are stored in the `docker-compose` files in the same directory as the OpenRAG `.env` file.
diff --git a/docs/docs/get-started/install-uvx.mdx b/docs/docs/get-started/install-uvx.mdx
index a165191f..4c565f65 100644
--- a/docs/docs/get-started/install-uvx.mdx
+++ b/docs/docs/get-started/install-uvx.mdx
@@ -44,7 +44,7 @@ For other installation methods, see [Select an installation method](/install-opt
    cd openrag-workspace
    ```
 
-2. Optional: If you want to use a pre-populated [OpenRAG `.env` file](/reference/configuration), copy it to this directory before invoking OpenRAG.
+2. Optional: If you want to use a pre-populated [OpenRAG `.env` file](/reference/configuration), create one at `~/.openrag/tui` before invoking OpenRAG.
 
 3. Invoke OpenRAG:
 
@@ -70,7 +70,7 @@ If you encounter errors during installation, see [Troubleshoot OpenRAG](/support
 When you install OpenRAG with `uvx`, you manage the OpenRAG services with the TUI.
 The TUI guides you through the initial configuration process before you start the OpenRAG services.
 
-Your configuration values are stored in an [OpenRAG `.env` file](/reference/configuration) that is created automatically in the OpenRAG installation directory, which is the directory where you invoked OpenRAG.
+Your configuration values are stored in an [OpenRAG `.env` file](/reference/configuration) that is created automatically at `~/.openrag/tui`.
 If OpenRAG detects an existing `.env` file in this directory, then the TUI can populate those values automatically during setup and onboarding.
 
 Container definitions are stored in the `docker-compose` files in the same directory as the OpenRAG `.env` file.
diff --git a/docs/docs/get-started/install.mdx b/docs/docs/get-started/install.mdx
index d044e48e..b1091905 100644
--- a/docs/docs/get-started/install.mdx
+++ b/docs/docs/get-started/install.mdx
@@ -69,7 +69,7 @@ If you encounter errors during installation, see [Troubleshoot OpenRAG](/support
 When you install OpenRAG with the installer script, you manage the OpenRAG services with the TUI.
 The TUI guides you through the initial configuration process before you start the OpenRAG services.
 
-Your configuration values are stored in an [OpenRAG `.env` file](/reference/configuration) that is created automatically in the OpenRAG installation directory, which is the directory where you ran the installer script.
+Your configuration values are stored in an [OpenRAG `.env` file](/reference/configuration) that is created automatically at `~/.openrag/tui`.
 If OpenRAG detects an existing `.env` file in this directory, then the TUI can populate those values automatically during setup and onboarding.
 
 Container definitions are stored in the `docker-compose` files in the same directory as the OpenRAG `.env` file.
diff --git a/docs/docs/get-started/manage-services.mdx b/docs/docs/get-started/manage-services.mdx
index 4ba0cc1d..d81beaee 100644
--- a/docs/docs/get-started/manage-services.mdx
+++ b/docs/docs/get-started/manage-services.mdx
@@ -8,6 +8,7 @@ import TabItem from '@theme/TabItem';
 import PartialDockerComposeUp from '@site/docs/_partial-docker-compose-up.mdx';
 import PartialDockerComposeDownAndPrune from '@site/docs/_partial-docker-compose-down-and-prune.mdx';
 import PartialFactorResetWarning from '@site/docs/_partial-factory-reset-warning.mdx';
+import PartialExportFlows from '@site/docs/_partial-export-flows.mdx';
 
 Service management is an essential part of maintaining your OpenRAG deployment.
 
@@ -120,67 +121,45 @@ See [Upgrade OpenRAG](/upgrade).
 
 ## Reset containers (destructive) {#reset-containers}
 
-Reset your OpenRAG deployment by recreating the containers and removing some related data.
-
-To completely reset your OpenRAG deployment and delete all OpenRAG data, see [Reinstall OpenRAG](/reinstall).
-
-### Export customized flows before resetting containers {#export-customized-flows-before-resetting-containers}
-
-If you modified the built-in flows or created custom flows in your OpenRAG Langflow instance, and you want to preserve those changes, [export your flows](https://docs.langflow.org/concepts-flows-import) before resetting your OpenRAG containers.
-
-### Factory Reset with the TUI
-
 <PartialFactorResetWarning />
 
-1. To destroy and recreate your OpenRAG containers, open the TUI's **Status** menu (<kbd>3</kbd>), and then click **Factory Reset**.
+Use these steps to reset your OpenRAG deployment by recreating the containers and deleting all data in the `~/.openrag` directory _except_ for the `.env` file and the `/documents` subdirectory.
 
-2. Repeat the [setup process](/install#setup) to restart the services and launch the OpenRAG app. Your OpenRAG passwords, OAuth credentials (if previously set), and onboarding configuration are restored from the `.env` file.
+This restores your OpenRAG deployment to a near-initial state while preserving your configuration (in `.env`) and uploaded documents (in `/documents`).
+Your documents are reingested into a fresh OpenSearch index after the reset.
 
-### Rebuild self-managed containers
+To reset your OpenRAG deployment _and_ delete all OpenRAG data, see [Reinstall OpenRAG](/reinstall).
 
-This command destroys and recreates the containers. Data stored exclusively on the containers is lost, such as Langflow flows.
+<Tabs>
+<TabItem value="TUI" label="TUI-managed services" default>
 
-If you want to preserve customized flows, see [Export customized flows before resetting containers](#export-customized-flows-before-resetting-containers).
+<PartialExportFlows />
 
-The `.env` file, `config` directory, `./openrag-documents` directory, `./opensearch-data` directory, and the `conversations.json` file are preserved.
+2. To destroy and recreate your OpenRAG containers, open the TUI's **Status** menu (<kbd>3</kbd>), and then click **Factory Reset**.
 
-```bash title="Docker"
-docker compose up --build --force-recreate --remove-orphans
-```
+3. Repeat the [setup process](/install#setup) to restart the services and launch the OpenRAG app. Your OpenRAG passwords, OAuth credentials (if previously set), and onboarding configuration are restored from the `.env` file.
 
-```bash title="Podman"
-podman compose up --build --force-recreate --remove-orphans
-```
+</TabItem>
+<TabItem value="env" label="Self-managed services">
 
-### Destroy and recreate self-managed containers
+<PartialExportFlows />
 
-Use separate commands to destroy and recreate the containers if you want to modify the configuration or delete other OpenRAG data before recreating the containers.
+2. Recreate the containers:
 
-:::warning
-These are destructive operations that reset your OpenRAG deployment to an initial state.
-Destroyed containers and deleted data are lost and cannot be recovered after running this operation.
-:::
+   ```bash title="Docker"
+   docker compose up --build --force-recreate --remove-orphans
+   ```
 
-1. Destroy the containers, volumes, and local images, and then remove (prune) any additional container objects:
+   ```bash title="Podman"
+   podman compose up --build --force-recreate --remove-orphans
+   ```
 
-   <PartialDockerComposeDownAndPrune />
+3. Launch the OpenRAG app, and then repeat the [application onboarding process](/docker#application-onboarding).
 
-2. Optional: Remove data that wasn't deleted by the previous commands:
+4. If you exported customized flows, [import your flows](https://docs.langflow.org/concepts-flows-import) into Langflow after completing the onboarding process.
 
-   * OpenRAG's `.env` file
-   * The contents of OpenRAG's `config` directory
-   * The contents of the `./openrag-documents` directory
-   * The contents of the `./opensearch-data` directory
-   * The `conversations.json` file
-
-3. If you deleted the `.env` file, prepare a new `.env` before redeploying the containers.
-For more information, see [Deploy OpenRAG with self-managed services](/docker).
-
-4. Recreate the containers:
-
-   <PartialDockerComposeUp />
-
-5. Launch the OpenRAG app, and then repeat the [application onboarding process](/docker#application-onboarding).
+</TabItem>
+</Tabs>
 
 ## See also
 
diff --git a/docs/docs/get-started/quickstart.mdx b/docs/docs/get-started/quickstart.mdx
index d040fd22..e006bea8 100644
--- a/docs/docs/get-started/quickstart.mdx
+++ b/docs/docs/get-started/quickstart.mdx
@@ -64,7 +64,7 @@ The script installs OpenRAG dependencies, including Docker or Podman, and then i
    Command completed successfully
    ```
 
-   Your OpenRAG configuration and passwords are stored in an [OpenRAG `.env` file](/reference/configuration) file that is created automatically in your OpenRAG installation directory, which is the directory where you ran the installer script.
+   Your OpenRAG configuration and passwords are stored in an [OpenRAG `.env` file](/reference/configuration) file that is created automatically at `~/.openrag/tui`.
    Container definitions are stored in the `docker-compose` files in the same directory.
 
 7. Under [**Native Services**](/manage-services), click **Start** to start the Docling service.
@@ -96,7 +96,7 @@ You can click a document to view the chunks of the document as they are stored i
 
    For this quickstart, use either the <Icon name="File" aria-hidden="true"/> **File** or <Icon name="Folder" aria-hidden="true"/> **Folder** upload options to load documents from your local machine.
    **Folder** uploads an entire directory.
-   The default directory is the `/openrag-documents` subdirectory in your OpenRAG installation directory.
+   The default directory is `~/.openrag/documents`.
 
    For information about the cloud storage provider options, see [Ingest files with OAuth connectors](/ingestion#oauth-ingestion).
 
@@ -121,7 +121,7 @@ You can click a document to view the chunks of the document as they are stored i
 
 2. For greater insight into the underlying [Langflow flow](/agents) that drives the OpenRAG chat, click **Edit in Langflow** and then click **Proceed** to launch the Langflow visual editor in a new browser window.
 
-   If Langflow requests login information, enter the `LANGFLOW_SUPERUSER` and `LANGFLOW_SUPERUSER_PASSWORD` from the `.env` file in your OpenRAG installation directory.
+   If Langflow requests login information, enter the `LANGFLOW_SUPERUSER` and `LANGFLOW_SUPERUSER_PASSWORD` from the `.env` file at `~/.openrag/tui`.
 
    The **OpenRAG OpenSearch Agent** flow opens in a new browser window.
 
diff --git a/docs/docs/get-started/reinstall.mdx b/docs/docs/get-started/reinstall.mdx
index d120f7cd..dc4466cb 100644
--- a/docs/docs/get-started/reinstall.mdx
+++ b/docs/docs/get-started/reinstall.mdx
@@ -8,6 +8,7 @@ import PartialDockerComposeDownAndPrune from '@site/docs/_partial-docker-compose
 import PartialDockerStopAll from '@site/docs/_partial-docker-stop-all.mdx';
 import PartialDockerRemoveAndCleanupSteps from '@site/docs/_partial-docker-remove-and-cleanup-steps.mdx';
 import PartialFactorResetWarning from '@site/docs/_partial-factory-reset-warning.mdx';
+import PartialExportFlows from '@site/docs/_partial-export-flows.mdx';
 
 You can reset your OpenRAG deployment to its initial state by recreating the containers and deleting accessory data, such as the `.env` file and ingested documents.
 
@@ -16,55 +17,50 @@ These are destructive operations that reset your OpenRAG deployment to an initia
 Destroyed containers and deleted data are lost and cannot be recovered after running these operations.
 :::
 
-## Export customized flows before reinstalling
-
-If you modified the built-in flows or created custom flows in your OpenRAG Langflow instance, and you want to preserve those changes, [export your flows](https://docs.langflow.org/concepts-flows-import) before reinstalling OpenRAG.
-
 ## Reinstall TUI-managed containers
 
-1. In the TUI's **Status** menu (<kbd>3</kbd>), click **Factory Reset** to destroy your OpenRAG containers and some related data.
+<PartialExportFlows />
+
+2. In the TUI's **Status** menu (<kbd>3</kbd>), click **Factory Reset** to [reset your OpenRAG containers](/manage-services#reset-containers).
 
    <PartialFactorResetWarning />
 
 2. Exit the TUI with <kbd>q</kbd>.
 
-3. Optional: Remove data that wasn't deleted by the **Factory Reset** operation.
-For a completely fresh installation, delete all of this data.
+3. Optional: Delete or edit [OpenRAG's `.env` file](/reference/configuration), which is stored at `~/.openrag/tui`.
 
-   * **OpenRAG's `.env` file**: Contains your OpenRAG configuration, including OpenRAG passwords, API keys, OAuth settings, and other [environment variables](/reference/configuration). If you delete this file, OpenRAG automatically generates a new one after you repeat the setup and onboarding process. Alternatively, you can add a prepopulated `.env` file to your OpenRAG installation directory before restarting OpenRAG.
-   * **The contents of the `./openrag-documents` directory**: Contains documents that you uploaded to OpenRAG. Delete these files to prevent documents from being reingested to your knowledge base after restarting OpenRAG. However, you might want to preserve OpenRAG's [default documents](https://github.com/langflow-ai/openrag/tree/main/openrag-documents).
+   This file contains your OpenRAG configuration, including OpenRAG passwords, API keys, OAuth settings, and other environment variables. If you delete this file, the TUI automatically generates a new one after you repeat the setup and onboarding process. If you preserve this file, the TUI can read values from the existing `.env` file during setup and onboarding.
 
-4. Restart the TUI with `uv run openrag` or `uvx openrag`.
+4. Optional: Remove any files from the `~/.openrag/documents` subdirectory that you don't want to reingest after redeploying the containers.
+It is recommended that you preserve OpenRAG's [default documents](https://github.com/langflow-ai/openrag/tree/main/openrag-documents).
 
-5. Repeat the [setup process](/install#setup) to configure OpenRAG and restart all services.
+5. Restart the TUI with `uv run openrag` or `uvx openrag`.
+
+6. Repeat the [setup process](/install#setup) to configure OpenRAG and restart all services.
 Then, launch the OpenRAG app and repeat the [application onboarding process](/install#application-onboarding).
 
-   If OpenRAG detects a `.env` file during setup and onboarding, it automatically populates any OpenRAG passwords, OAuth credentials, and onboarding configuration set in that file.
-
 ## Reinstall self-managed containers with `docker compose` or `podman compose`
 
 Use these steps to reinstall OpenRAG containers with streamlined `docker compose` or `podman compose` commands:
 
-1. Destroy the containers, volumes, and local images, and then remove (prune) any additional container objects:
+<PartialExportFlows />
+
+2. Destroy the containers, volumes, and local images, and then remove (prune) any additional container objects.
+
+   <PartialFactorResetWarning />
 
    <PartialDockerComposeDownAndPrune />
 
-2. Optional: Remove data that wasn't deleted by the previous commands:
+3. Optional: Edit OpenRAG's `.env` file if needed.
 
-   * OpenRAG's `.env` file
-   * The contents of OpenRAG's `config` directory
-   * The contents of the `./openrag-documents` directory
-   * The contents of the `./opensearch-data` directory
-   * The `conversations.json` file
+4. Optional: Remove any files from the `~/.openrag/documents` subdirectory that you don't want to reingest after redeploying the containers.
+It is recommended that you preserve OpenRAG's [default documents](https://github.com/langflow-ai/openrag/tree/main/openrag-documents).
 
-3. If you deleted the `.env` file, prepare a new `.env` before redeploying the containers.
-For more information, see [Deploy OpenRAG with self-managed services](/docker).
-
-4. Redeploy OpenRAG:
+5. Redeploy OpenRAG:
 
    <PartialDockerComposeUp />
 
-5. Launch the OpenRAG app, and then repeat the [application onboarding process](/docker#application-onboarding).
+6. Launch the OpenRAG app, and then repeat the [application onboarding process](/docker#application-onboarding).
 
 ## Reinstall self-managed containers with discrete `docker` or `podman` commands
 
@@ -72,19 +68,18 @@ Use these commands to remove and clean up OpenRAG containers with discrete `dock
 
 If you want to reinstall one container, specify the container name in the commands instead of running the commands on all containers.
 
-1. Stop all running containers:
+<PartialExportFlows />
+
+2. Stop all running containers:
 
    <PartialDockerStopAll />
 
 <PartialDockerRemoveAndCleanupSteps />
 
-7. Optional: Remove data that wasn't deleted by the previous commands:
+8. Optional: Edit OpenRAG's `.env` file if needed.
 
-   * OpenRAG's `.env` file
-   * The contents of OpenRAG's `config` directory
-   * The contents of the `./openrag-documents` directory
-   * The contents of the `./opensearch-data` directory
-   * The `conversations.json` file
+9. Optional: If you removed all containers or specifically the OpenSearch container, then you can remove any files from the `~/.openrag/documents` subdirectory that you don't want to reingest after redeploying the containers.
+It is recommended that you preserve OpenRAG's [default documents](https://github.com/langflow-ai/openrag/tree/main/openrag-documents).
 
-8. If you removed all OpenRAG containers, [redeploy OpenRAG](/docker).
+10. If you removed all OpenRAG containers, [redeploy OpenRAG](/docker).
 If you removed only one container, redeploy that container with the appropriate `docker run` or `podman run` command.
\ No newline at end of file
diff --git a/docs/docs/get-started/tui.mdx b/docs/docs/get-started/tui.mdx
index 0965478b..619543e3 100644
--- a/docs/docs/get-started/tui.mdx
+++ b/docs/docs/get-started/tui.mdx
@@ -10,7 +10,7 @@ The OpenRAG Terminal User Interface (TUI) provides a simplified and guided exper
 If you install OpenRAG with the [automatic installer script](/install), [`uv`](/install-uv), or [`uvx`](/install-uvx), you use the TUI to manage your OpenRAG deployment.
 The TUI guides you through the initial setup, automatically manages your OpenRAG `.env` and `docker-compose` files, and provides convenient access to [service management](/manage-services) controls.
 
-In contrast, when you [deploy OpenRAG with self-managed services](/docker), you must manually configure OpenRAG by preparing a `.env` file and using Docker or Podman commands to deploy and manage your OpenRAG services.
+In contrast, when you [deploy OpenRAG with self-managed services](/docker), you must manually configure OpenRAG by preparing a `.env` file, and then use Docker or Podman commands to deploy and manage your OpenRAG services.
 
 ## Access the TUI {#access-the-tui}
 
diff --git a/docs/docs/get-started/uninstall.mdx b/docs/docs/get-started/uninstall.mdx
index 3ffd3670..a7865395 100644
--- a/docs/docs/get-started/uninstall.mdx
+++ b/docs/docs/get-started/uninstall.mdx
@@ -29,13 +29,7 @@ Use these steps to uninstall a self-managed OpenRAG deployment with streamlined
 
    <PartialDockerComposeDownAndPrune />
 
-2. Remove data that wasn't deleted by the previous commands:
-
-   * OpenRAG's `.env` file
-   * The contents of OpenRAG's `config` directory
-   * The contents of the `./openrag-documents` directory
-   * The contents of the `./opensearch-data` directory
-   * The `conversations.json` file
+2. Remove OpenRAG's `.env` file and the `~/.openrag/documents` directory, which aren't deleted by the previous commands.
 
 3. Stop `docling-serve`:
 
@@ -53,13 +47,7 @@ Use these commands to uninstall a self-managed OpenRAG deployment with discrete
 
 <PartialDockerRemoveAndCleanupSteps />
 
-7. Remove data that wasn't deleted by the previous commands:
-
-   * OpenRAG's `.env` file
-   * The contents of OpenRAG's `config` directory
-   * The contents of the `./openrag-documents` directory
-   * The contents of the `./opensearch-data` directory
-   * The `conversations.json` file
+7. Remove OpenRAG's `.env` file and the `~/.openrag/documents` directory, which aren't deleted by the previous commands.
 
 8. Stop `docling-serve`:
 
diff --git a/docs/docs/get-started/upgrade.mdx b/docs/docs/get-started/upgrade.mdx
index 22808116..611c6f6b 100644
--- a/docs/docs/get-started/upgrade.mdx
+++ b/docs/docs/get-started/upgrade.mdx
@@ -5,6 +5,7 @@ slug: /upgrade
 
 import Tabs from '@theme/Tabs';
 import TabItem from '@theme/TabItem';
+import PartialExportFlows from '@site/docs/_partial-export-flows.mdx';
 
 Use these steps to upgrade your OpenRAG deployment to the latest version or a specific version.
 
@@ -21,12 +22,14 @@ Upgrading the Python package also upgrades Docling by bumping the dependency in
 
 This is a two-part process because upgrading the OpenRAG Python package updates the Terminal User Interface (TUI) and Python code, but the container versions are controlled by environment variables in your [OpenRAG `.env` file](/reference/configuration).
 
-1. To check for updates, open the TUI's **Status** menu (<kbd>3</kbd>), and then click **Upgrade**.
+<PartialExportFlows />
 
-2. If there is an update, stop all OpenRAG services.
+2. To check for updates, open the TUI's **Status** menu (<kbd>3</kbd>), and then click **Upgrade**.
+
+3. If there is an update, stop all OpenRAG services.
 In the **Status** menu, click **Stop Services**.
 
-3. Upgrade the OpenRAG Python package to the latest version from [PyPI](https://pypi.org/project/openrag/).
+4. Upgrade the OpenRAG Python package to the latest version from [PyPI](https://pypi.org/project/openrag/).
 The commands to upgrade the package depend on how you installed OpenRAG.
 
    <Tabs>
@@ -109,12 +112,12 @@ The commands to upgrade the package depend on how you installed OpenRAG.
    </TabItem>
    </Tabs>
 
-4. In the OpenRAG TUI, click **Start All Services**, and then wait while the upgraded containers start.
+5. In the OpenRAG TUI, click **Start All Services**, and then wait while the upgraded containers start.
 
    When you start services after upgrading the Python package, OpenRAG runs `docker compose pull` to get the appropriate container images matching the version specified in your OpenRAG `.env` file. Then, it recreates the containers with the new images using `docker compose up -d --force-recreate`.
 
    :::tip Pin container versions
-   In the `.env` file, the `OPENRAG_VERSION` [environment variable](/reference/configuration#system-settings) is set to `latest` by default, which pulls the `latest` available container images.
+   In the OpenRAG `.env` file, the `OPENRAG_VERSION` [environment variable](/reference/configuration#system-settings) is set to `latest` by default, which pulls the `latest` available container images.
    To pin a specific container image version, you can set `OPENRAG_VERSION` to the desired container image version, such as `OPENRAG_VERSION=0.1.33`.
 
    However, when you upgrade the Python package, OpenRAG automatically attempts to keep the `OPENRAG_VERSION` synchronized with the Python package version.
@@ -124,24 +127,27 @@ The commands to upgrade the package depend on how you installed OpenRAG.
 
    If you get an error that `langflow container already exists` error during upgrade, see [Langflow container already exists during upgrade](/support/troubleshoot#langflow-container-already-exists-during-upgrade).
 
-5. Under [**Native Services**](/manage-services), click **Start** to start the Docling service.
+6. Under [**Native Services**](/manage-services), click **Start** to start the Docling service.
 
-6. When the upgrade process is complete, you can close the **Status** window and continue using OpenRAG.
+7. When the upgrade process is complete, you can close the **Status** window and continue using OpenRAG.
 
 ## Upgrade self-managed containers
 
-To fetch and apply the latest container images while preserving your OpenRAG data, run the commands for your container management tool.
-By default, OpenRAG's `docker-compose` files pull the latest container images.
+<PartialExportFlows />
 
-```bash title="Docker"
-docker compose pull
-docker compose up -d --force-recreate
-```
+2. Fetch and apply the latest container images while preserving your OpenRAG data:
 
-```bash title="Podman"
-podman compose pull
-podman compose up -d --force-recreate
-```
+   ```bash title="Docker"
+   docker compose pull
+   docker compose up -d --force-recreate
+   ```
+
+   ```bash title="Podman"
+   podman compose pull
+   podman compose up -d --force-recreate
+   ```
+
+   By default, OpenRAG's `docker-compose` files pull the latest container images.
 
 ## See also
 
diff --git a/docs/docs/reference/configuration.mdx b/docs/docs/reference/configuration.mdx
index 9a36ebaa..444bab0d 100644
--- a/docs/docs/reference/configuration.mdx
+++ b/docs/docs/reference/configuration.mdx
@@ -5,62 +5,40 @@ slug: /reference/configuration
 
 import PartialDockerComposeUp from '@site/docs/_partial-docker-compose-up.mdx';
 
-OpenRAG recognizes environment variables from the following sources:
+OpenRAG's `.env` file is the primary configuration file for OpenRAG.
+Environment variables in `.env` always take precedence over other sources.
 
-* [Environment variables](#configure-environment-variables): Values set in the `.env` file in the OpenRAG installation directory.
-* [Langflow runtime overrides](#langflow-runtime-overrides): Langflow components can set environment variables at runtime.
-* [Default or fallback values](#default-values-and-fallbacks): These values are default or fallback values if OpenRAG doesn't find a value.
+For deployments managed with the Terminal User Interface (TUI), this file is located at `~/.openrag/tui`, and it can be created automatically during [installation](/install-options).
 
-## Configure environment variables
+For [self-managed deployments](/docker), this file can be located at the root of your OpenRAG project directory or referenced from another location.
 
-Environment variables are set in a `.env` file in the root of your OpenRAG project directory.
+For an example, see [`.env.example` in the OpenRAG repository](https://github.com/langflow-ai/openrag/blob/main/.env.example).
 
-For an example `.env` file, see [`.env.example` in the OpenRAG repository](https://github.com/langflow-ai/openrag/blob/main/.env.example).
+:::tip
+OpenRAG's Docker Compose files are populated automatically using values from the `.env` file, so you don't need to edit the Docker Compose files manually.
+:::
 
-The Docker Compose files are populated with values from your `.env`, so you don't need to edit the Docker Compose files manually.
+If a variable isn't set, OpenRAG uses default or fallback values where available.
+Not all variables have default values, and errors can occur if required variables aren't set.
+Default values can be found in the reference tables on this page and in [`config_manager.py`](https://github.com/langflow-ai/openrag/blob/main/src/config/config_manager.py), [`settings.py`](https://github.com/langflow-ai/openrag/blob/main/src/config/settings.py), and [`logging_config.py`](https://github.com/langflow-ai/openrag/blob/main/src/utils/logging_config.py).
 
-Environment variables always take precedence over other variables.
+You can [temporarily set Langflow variables at runtime](#modify-a-flow-at-runtime).
+However, these temporary overrides don't overlap with most OpenRAG environment variables.
+The only exceptions are flow-level Langflow settings, such as the language model used in a flow.
 
-### Set environment variables {#set-environment-variables}
+## Edit the `.env` file {#set-environment-variables}
 
-Environment variables are either mutable or immutable.
+During [installation](/install-options), an initial `.env` file is created automatically or manually.
+You can edit this file to change OpenRAG configuration settings after installation.
 
-If you edit mutable environment variables, you can apply the changes by stopping and restarting the OpenRAG services after editing the `.env` file:
+Each OpenRAG environment variable is either mutable or immutable.
+This determines the actions you must take to apply changes after editing the `.env` file:
 
-1. [Stop the OpenRAG services](/manage-services).
+* **Mutable environment variables**: You can apply changes to mutable environment variables by [stopping and restarting the OpenRAG services](/manage-services) after editing the `.env` file.
 
-2. Edit your `.env` file.
+* **Immutable environment variables**: You must [redeploy OpenRAG](/reinstall) with your modified `.env` file if you change immutable environment variables.
 
-3. [Restart the OpenRAG services](/manage-services).
-
-If you edit immutable environment variables, you must [redeploy OpenRAG](/reinstall) with your modified `.env` file.
-For example, with self-managed services, do the following:
-
-1. Stop the deployment:
-
-   ```bash title="Docker"
-   docker compose down
-   ```
-
-   ```bash title="Podman"
-   podman compose down
-   ```
-
-2. Edit your `.env` file.
-
-3. Redeploy OpenRAG:
-
-   <PartialDockerComposeUp />
-
-4. Restart the Docling service.
-
-5. Launch the OpenRAG app, and then repeat the [application onboarding process](/install#application-onboarding). The values in your `.env` file are automatically populated.
-
-## Supported environment variables
-
-All OpenRAG configuration can be controlled through environment variables.
-
-### Model provider settings {#model-provider-settings}
+## Model provider settings {#model-provider-settings}
 
 Configure which models and providers OpenRAG uses to generate text and embeddings.
 You only need to provide credentials for the providers you are using in OpenRAG.
@@ -80,7 +58,7 @@ Some of these variables are immutable and can only be changed by redeploying Ope
 | `WATSONX_ENDPOINT` | Not set | Custom provider endpoint for the IBM watsonx.ai model provider. |
 | `WATSONX_PROJECT_ID` | Not set | Project ID for the IBM watsonx.ai model provider. |
 
-### Document processing settings {#document-processing-settings}
+## Document processing settings {#document-processing-settings}
 
 Control how OpenRAG [processes and ingests documents](/ingestion) into your knowledge base.
 
@@ -91,10 +69,10 @@ Control how OpenRAG [processes and ingests documents](/ingestion) into your know
 | `DISABLE_INGEST_WITH_LANGFLOW` | `false` | Disable Langflow ingestion pipeline. |
 | `DOCLING_OCR_ENGINE` | Set by OS | OCR engine for document processing. For macOS, `ocrmac`. For any other OS, `easyocr`. |
 | `OCR_ENABLED` | `false` | Enable OCR for image processing. |
-| `OPENRAG_DOCUMENTS_PATHS` | `./openrag-documents` | Document paths for ingestion. |
+| `OPENRAG_DOCUMENTS_PATHS` | `~/.openrag/documents` | Document paths for ingestion. |
 | `PICTURE_DESCRIPTIONS_ENABLED` | `false` | Enable picture descriptions. |
 
-### Langflow settings {#langflow-settings}
+## Langflow settings {#langflow-settings}
 
 Configure the OpenRAG Langflow server's authentication, contact point, and built-in flow definitions.
 
@@ -120,7 +98,7 @@ For better security, it is recommended to set `LANGFLOW_SUPERUSER_PASSWORD` so t
 | `LANGFLOW_CHAT_FLOW_ID`, `LANGFLOW_INGEST_FLOW_ID`, `NUDGES_FLOW_ID` | Built-in flow IDs | These variables are set automatically to the IDs of the chat, ingestion, and nudges [flows](/agents). The default values are found in [`.env.example`](https://github.com/langflow-ai/openrag/blob/main/.env.example). Only change these values if you want to replace a built-in flow with your own custom flow. The flow JSON must be present in your version of the OpenRAG codebase. For example, if you [deploy self-managed services](/docker), you can add the flow JSON to your local clone of the OpenRAG repository before deploying OpenRAG. |
 | `SYSTEM_PROMPT` | `You are a helpful AI assistant with access to a knowledge base. Answer questions based on the provided context.` | System prompt instructions for the agent driving the **Chat** flow. |
 
-### OAuth provider settings
+## OAuth provider settings
 
 Configure [OAuth providers](/ingestion#oauth-ingestion) and external service integrations.
 
@@ -131,7 +109,7 @@ Configure [OAuth providers](/ingestion#oauth-ingestion) and external service int
 | `MICROSOFT_GRAPH_OAUTH_CLIENT_ID`<br/>`MICROSOFT_GRAPH_OAUTH_CLIENT_SECRET` | Not set | Enable the [Microsoft Graph OAuth client](https://learn.microsoft.com/en-us/onedrive/developer/rest-api/getting-started/graph-oauth) integration by providing [Azure application registration credentials for SharePoint and OneDrive](https://learn.microsoft.com/en-us/onedrive/developer/rest-api/getting-started/app-registration?view=odsp-graph-online). |
 | `WEBHOOK_BASE_URL` | Not set | Base URL for OAuth connector webhook endpoints. If this variable isn't set, a default base URL is used. |
 
-### OpenSearch settings
+## OpenSearch settings
 
 Configure OpenSearch database authentication.
 
@@ -142,7 +120,7 @@ Configure OpenSearch database authentication.
 | `OPENSEARCH_USERNAME` | `admin` | OpenSearch administrator username. |
 | `OPENSEARCH_PASSWORD` | Must be set at start up | Required. OpenSearch administrator password. Must adhere to the [OpenSearch password complexity requirements](https://docs.opensearch.org/latest/security/configuration/demo-configuration/#setting-up-a-custom-admin-password). You must set this directly in the `.env` or in the TUI's [**Basic/Advanced Setup**](/install#setup). |
 
-### System settings
+## System settings
 
 Configure general system components, session management, and logging.
 
@@ -156,23 +134,4 @@ Configure general system components, session management, and logging.
 | `MAX_WORKERS` | `1` | Maximum number of workers for document processing. |
 | `OPENRAG_VERSION` | `latest` | The version of the OpenRAG Docker images to run. For more information, see [Upgrade OpenRAG](/upgrade) |
 | `SERVICE_NAME` | `openrag` | Service name for logging. |
-| `SESSION_SECRET` | Automatically generated | Session management. |
-
-## Langflow runtime overrides
-
-You can modify [flow](/agents) settings at runtime without permanently changing the flow's configuration.
-
-Runtime overrides are implemented through _tweaks_, which are one-time parameter modifications that are passed to specific Langflow components during flow execution.
-
-For more information on tweaks, see the Langflow documentation on [Input schema (tweaks)](https://docs.langflow.org/concepts-publish#input-schema).
-
-## Default values and fallbacks
-
-If a variable isn't set by environment variables or a configuration file, OpenRAG can use a default value if one is defined in the codebase.
-Default values can be found in the OpenRAG repository:
-
-* OpenRAG configuration: [`config_manager.py`](https://github.com/langflow-ai/openrag/blob/main/src/config/config_manager.py)
-
-* System configuration: [`settings.py`](https://github.com/langflow-ai/openrag/blob/main/src/config/settings.py)
-
-* Logging configuration: [`logging_config.py`](https://github.com/langflow-ai/openrag/blob/main/src/utils/logging_config.py)
\ No newline at end of file
+| `SESSION_SECRET` | Automatically generated | Session management. |
\ No newline at end of file
diff --git a/docs/docs/support/troubleshoot.mdx b/docs/docs/support/troubleshoot.mdx
index 958fa102..0bb7b141 100644
--- a/docs/docs/support/troubleshoot.mdx
+++ b/docs/docs/support/troubleshoot.mdx
@@ -68,7 +68,7 @@ This is likely due to a stale `uv` cache when you [install OpenRAG with `uvx`](/
 
 When you invoke OpenRAG with `uvx openrag`, `uvx` creates a cached, ephemeral environment that doesn't modify your project.
 The location and path of this cache depends on your operating system.
-For example, on macOS, this is typically a user cache directory, such as `/Users/USER_NAME/.cache/uv`.
+For example, on macOS, this is typically a user cache directory, such as `~/.cache/uv`.
 
 This cache can become stale, producing errors like missing dependencies.