docs: update documentation changes

docs: updated source control

docs: fixed formatting

docs: removed irrelevant files

fix: build

Author: xrissoula

docs/Getting-Started/polykey-cli/README.md

@@ -49,9 +49,13 @@ tickets in the
 
 Start your journey with Polykey by following the tutorials below in sequence:
 
-:::tip For a visual walkthrough, check out our
+:::tip Tip
+
+For a visual walkthrough, check out our
 [getting started demo video](https://vimeo.com/884649667) after installing
-Polykey. :::
+Polykey. 
+
+:::
 
 1. **[Installation](/docs/tutorials/polykey-cli/installation)** - Install
    Polykey CLI on your platform.

docs/Getting-Started/polykey-cli/managing-multiple-nodes.md

@@ -70,7 +70,7 @@ specify a node path, so it automatically targets the default node path.
 **Shell B (for your new node, nodeB):**
 
 ```bash
-polykey agent super_start --node-path ./nodeB --background
+polykey agent start --node-path ./nodeB --background
 ```
 
 This command starts a new Polykey agent for nodeB in the background. The first

docs/Getting-Started/polykey-cli/managing-secrets.md

@@ -111,15 +111,13 @@ we created in the previous example.
 API_ACCESS_KEY
 ```
 
-:::note
-
-### Secure Deletion of Local Secrets
+:::note Secure Deletion of Local Secrets
 
 After adding a secret to a vault, securely delete the local copy if it's no
 longer needed. This ensures that no unsecured traces of sensitive information
 remain on your local filesystem. :::
 
-## Retreiving Secrets
+ Retreiving Secrets
 
 Retrieve a secret from the given vault using the polykey secrets get command.
 This command accesses the encrypted content within a vault and outputs it,
@@ -225,13 +223,14 @@ vault.
 polykey secrets mkdir <vaultName>:<directoryPath>
 ```
 
-#### Example: Creating a Directory in a Vault
+:::note Example: Creating a Directory in a Vault
 
 To create a directory named "NFTs" within the "my-image-vault":
 
 ```bash
 polykey secrets mkdir my-image-vault:NFTs
 ```
+:::note
 
 ### Adding a Secret to a Directory in a Vault
 
@@ -306,14 +305,14 @@ To view metadata about a secret:
 polykey secrets stat <vaultName>:<secretName>
 ```
 
-#### Example: Viewing Metadata for a Secret
+:::note Note
+
+Example: Viewing Metadata for a Secret
 
 ```bash
 polykey secrets stat my-image-vault:NFTs/Dali.png
 ```
 
-#### Example Output
-
 ```bash
 -> polykey nodes connections                                               
 host                                   	hostname	nodeIdEncoded                                        	port	timeout	usageCount	authenticated
@@ -350,14 +349,18 @@ To remove a secret from a vault:
 polykey secrets rm <vaultName>:<secretName>
 ```
 
-#### Example: Deleting a Secret
+:::note Note
+ Example: Deleting a Secret
 
 $ polykey secrets ls my-image-vault:nfts
 nfts/dali.png
 nfts/some-image.png
 
 $ polykey secrets rm my-image-vault:nfts/some-image.png
-# note the lack of output
+
+Note the lack of output
+
+:::note
 
 $ polykey secrets ls my-image-vault:nfts
 nfts/dali.png

docs/Getting-Started/polykey-cli/managing-vaults.md

@@ -55,7 +55,7 @@ If you need to remove a vault, you can delete it using the delete command:
 polykey vaults delete <vaultName>
 ```
 
-#### Example
+:::note Example
 
 Delete the vault named myvault:
 
@@ -66,6 +66,7 @@ polykey vaults rm myvault
 This operation does not produce output on successful execution, indicating the
 vault has been removed.
 
+:::note
 ## Viewing Vault History
 
 Each vault maintains a version history which tracks changes over time. Use the

docs/Getting-Started/polykey-cli/sharing-vaults.md

@@ -73,14 +73,16 @@ polykey vaults scan <nodeId>
 
 - `<nodeId>`: The Node ID of the node that shared the vault with you.
 
-#### Example
+:::note Example
 
 ```bash
 polykey vaults scan v4c11qv5fpq2fm3ropmma2sglfc9349jspqb1iutl3f7en1ckv500
 ```
 
 This command lists the vaults shared by the specified node.
 
+:::note
+
 ## Cloning the Shared Vault
 
 After identifying the shared vaults, the recipient can clone the desired vault
@@ -93,12 +95,14 @@ polykey vaults clone <vaultName> <nodeId>
 - `<vaultName>`: The name of the vault to be cloned.
 - `<nodeId>`: The Node ID from which to clone the vault.
 
-### Example
+:::note Example
 
 ```bash
 polykey vaults clone myvault v4c11qv5fpq2fm3ropmma2sglfc9349jspqb1iutl3f7en1ckv500
 ```
 
+:::note
+
 This command clones "myvault" from the specified node to the local system.
 
 ## Synchronizing Changes
@@ -114,14 +118,16 @@ polykey vaults pull <vaultName> <targetNodeId>
 - `<vaultNameOrId>`: The name or ID of the vault to update.
 - `<targetNodeId>`: (Optional) The node ID from which to pull updates.
 
-### Example
+:::note Example
 
 ```bash
 polykey vaults pull myvault v4c11qv5fpq2fm3ropmma2sglfc9349jspqb1iutl3f7en1ckv500
 ```
 
 This command updates "myvault" with the latest changes from the specified node.
 
+:::note
+
 ## Conclusion
 
 Sharing and synchronizing vaults in Polykey enhances collaboration and security

docs/Getting-Started/polykey-cli/using-environment-variables.md

@@ -132,7 +132,7 @@ management of environment variables. It allows for the dynamic and secure
 handling of sensitive data across different stages of development and
 deployment.
 
-## Additional References
+:::note Additional References
 
 We encourage you to delve deeper into Polykey and consider integrating it into
 your workflows. For further insights and to participate in community
@@ -144,6 +144,8 @@ discussions, please explore the following resources:
 - [Using Polykey for secure access to cloud providers:](https://polykey.com/blog/introducing-a-new-standard-in-environment-secrets-management-with-polykey)
   Learn how Polykey facilitates secure interactions with cloud services.
 
+:::note
+
 ## Tying It All Together
 
 **1. Initial Setup by User A:**

docs/Getting-Started/polykey-core/README.md

@@ -65,7 +65,11 @@ $ polykey secrets dir ~/test-dir vault1
 3. If the edited file isn't saved or the editor crashes, the secret will not be
    written
 
-:::warning This command does not work on Windows yet :::
+:::warning Warning
+
+This command does not work on Windows yet 
+
+:::
 
 Usage:
 
@@ -85,7 +89,11 @@ I edited this secret inside an editor
 4. If no paths are specified, this command takes input from `stdin` and prints
    it to `stdout`
 
-:::tip `^D` in the terminal stands for the key combination 'Ctrl-D' :::
+:::tip Tip 
+
+`^D` in the terminal stands for the key combination 'Ctrl-D' 
+
+:::
 
 Usage:
 
@@ -184,7 +192,11 @@ new-name
 1. Get the stats of a specified secret from a vault
 2. Requires secret location (vaultName:secretName) as a parameter
 
-:::note The mode (or file permissions) doesn't exist within a vault :::
+:::note Note
+
+ The mode (or file permissions) doesn't exist within a vault 
+
+:::
 
 Usage:
 
@@ -213,7 +225,10 @@ blocks: 1
 2. Run a command with the specified variables, or export them in the current
    working environment
 
-:::note Separate the environment variables from the command by passing in a `--`
+:::note Note
+
+Separate the environment variables from the command by passing in a `--`
+
 :::
 
 Usage:
@@ -253,11 +268,15 @@ do not commit your keys to github
 1. Reads input from `stdin` and writes it to the specified file
 2. If the file doesn't exist, it gets created
 
-:::tip `stdin`, or standard input, can be either manually entered by typing, or
+:::tip Tip
+
+`stdin`, or standard input, can be either manually entered by typing, or
 piped in through another command.
 
 To close the input steam and save the file, press `^D`, or 'Ctrl-D' in a new
-line, or press `^D` twice on the same line. :::
+line, or press `^D` twice on the same line. 
+
+:::
 
 Usage: