docs: re-index chapters in the CLI references (more flat approach) (#525)

* docs: re-index chapters in the CLI reference (more flat approach)

Signed-off-by: David Dal Busco <david.dalbusco@outlook.com>

* 📄 Update LLMs.txt snapshot for PR review

---------

Signed-off-by: David Dal Busco <david.dalbusco@outlook.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Author: peterpeterparker

.llms-snapshots/llms-full.txt

@@ -7603,9 +7603,9 @@ npm i -g @junobuild/cli
 
 ---
 
-## Administration
+## Commands
 
-Commands dedicated to configuring and managing deployed Satellites, Mission Control, and other modules.
+The following is a complete list of commands available in the Juno CLI.
 
 **Tip:**
 
@@ -7683,6 +7683,20 @@ Usage: juno deploy [options]Options:  --batch               Number of files to u
 
 ---
 
+### Clear
+
+Clear existing app code by removing JavaScript, HTML, CSS, and other files from your satellite.
+
+```
+Usage: juno clear [options]Options:  -f, --fullPath        Clear a particular file of your app.  -m, --mode            Choose which environment to use (production, staging, development). Defaults to production if omitted.  -p, --profile         Specify an optional profile to use (e.g. personal, team). Useful when managing multiple Mission Controls.  --container-url       Override a custom container URL. If not provided, defaults to production or the local container in development mode.  --console-url         Specify a custom URL to access the developer Console.  -h, --help            Output usage information.
+```
+
+**Note:**
+
+This command removes existing files from the satellite and only affects the app assets. The user's uploaded files will not be cleared as the app is deployed to a reserved collection, `#dapp`.
+
+---
+
 ### Config
 
 Apply configuration to satellite.
@@ -7723,20 +7737,6 @@ Usage: juno start [options]Options:  -t, --target          Which module type sho
 
 ---
 
-### Clear
-
-Clear existing app code by removing JavaScript, HTML, CSS, and other files from your satellite.
-
-```
-Usage: juno clear [options]Options:  -f, --fullPath        Clear a particular file of your app.  -m, --mode            Choose which environment to use (production, staging, development). Defaults to production if omitted.  -p, --profile         Specify an optional profile to use (e.g. personal, team). Useful when managing multiple Mission Controls.  --container-url       Override a custom container URL. If not provided, defaults to production or the local container in development mode.  --console-url         Specify a custom URL to access the developer Console.  -h, --help            Output usage information.
-```
-
-**Note:**
-
-This command removes existing files from the satellite and only affects the app assets. The user's uploaded files will not be cleared as the app is deployed to a reserved collection, `#dapp`.
-
----
-
 ### Upgrade
 
 Upgrade a module to a new version.
@@ -7754,7 +7754,7 @@ The CLI automatically runs in non-interactive mode if either a JUNO\_TOKEN is se
 
 ---
 
-## Changes
+### Changes
 
 Review and apply changes submitted to your module.
 
@@ -7764,7 +7764,7 @@ Usage: juno changes <subcommand> [options]Subcommands:  apply               Appl
 
 ---
 
-### Apply
+#### Apply
 
 Apply a submitted change.
 
@@ -7774,7 +7774,7 @@ Usage: juno changes apply [options]Options:  -i, --id              The ID of the
 
 ---
 
-### List
+#### List
 
 List all submitted or applied changes.
 
@@ -7784,7 +7784,7 @@ Usage: juno changes list [options]Options:  -a, --all           Search through a
 
 ---
 
-### Reject
+#### Reject
 
 Reject a change.
 
@@ -7794,7 +7794,7 @@ Usage: juno changes reject [options]Options:  -i, --id              The ID of th
 
 ---
 
-## Emulator
+### Emulator
 
 Handle developer tasks like starting/stopping a local network.
 
@@ -7804,7 +7804,7 @@ Usage: juno dev <subcommand> [options]Subcommands:  start               Start a
 
 ---
 
-### Start
+#### Start
 
 Start a local Internet Computer network in a container.
 
@@ -7814,7 +7814,7 @@ Usage: juno dev start [options]Options:  -l, --lang            Specify the langu
 
 ---
 
-### Wait
+#### Wait
 
 Wait until the emulator is ready.
 
@@ -7824,7 +7824,7 @@ Usage: juno dev wait [options]Options:  -t, --timeout         Timeout for the em
 
 ---
 
-## Functions
+### Functions
 
 Build and upgrade your satellite's serverless functions.
 
@@ -7834,17 +7834,7 @@ Usage: juno functions <subcommand> [options]Subcommands:  build                B
 
 ---
 
-## Run
-
-Run a custom script in the CLI context.
-
-```
-Usage: juno run [options]Options:  -s, --src        The path to your JavaScript or TypeScript script.  -m, --mode            Choose which environment to use (production, staging, development). Defaults to production if omitted.  -p, --profile         Specify an optional profile to use (e.g. personal, team). Useful when managing multiple Mission Controls.  --container-url       Override a custom container URL. If not provided, defaults to production or the local container in development mode.  -h, --help            Output usage information.
-```
-
----
-
-### Build
+#### Build
 
 Build your serverless functions.
 
@@ -7854,7 +7844,7 @@ Usage: juno functions build [options]Options:  -l, --lang            Specify the
 
 ---
 
-### Eject
+#### Eject
 
 Generate the required files to begin developing serverless functions in your project.
 
@@ -7864,7 +7854,7 @@ Usage: juno functions eject [options]Options:  -l, --lang            Specify the
 
 ---
 
-### Publish
+#### Publish
 
 Publish a new version of your serverless functions.
 
@@ -7874,7 +7864,7 @@ Usage: juno functions publish [options]Options:  --no-apply            Submit th
 
 ---
 
-### Upgrade
+#### Upgrade
 
 Upgrade your serverless functions.
 
@@ -7884,9 +7874,13 @@ Usage: juno functions upgrade [options]Options:  --cdn                 Select a
 
 ---
 
-## Others
+### Run
 
-Additional commands for managing and interacting with the CLI environment.
+Run a custom script in the CLI context.
+
+```
+Usage: juno run [options]Options:  -s, --src        The path to your JavaScript or TypeScript script.  -m, --mode            Choose which environment to use (production, staging, development). Defaults to production if omitted.  -p, --profile         Specify an optional profile to use (e.g. personal, team). Useful when managing multiple Mission Controls.  --container-url       Override a custom container URL. If not provided, defaults to production or the local container in development mode.  -h, --help            Output usage information.
+```
 
 ---
 

docs/reference/cli.mdx

@@ -27,9 +27,9 @@ npm i -g @junobuild/cli
 
 ---
 
-## Administration
+## Commands
 
-Commands dedicated to configuring and managing deployed Satellites, Mission Control, and other modules.
+The following is a complete list of commands available in the Juno CLI.
 
 :::tip
 
@@ -107,6 +107,20 @@ import Deploy from "./cli/deploy.md";
 
 ---
 
+### Clear
+
+import Clear from "./cli/clear.md";
+
+<Clear />
+
+:::note
+
+This command removes existing files from the satellite and only affects the app assets. The user's uploaded files will not be cleared as the app is deployed to a reserved collection, `#dapp`.
+
+:::
+
+---
+
 ### Config
 
 import Config from "./cli/config.md";
@@ -139,20 +153,6 @@ import Start from "./cli/start.md";
 
 ---
 
-### Clear
-
-import Clear from "./cli/clear.md";
-
-<Clear />
-
-:::note
-
-This command removes existing files from the satellite and only affects the app assets. The user's uploaded files will not be cleared as the app is deployed to a reserved collection, `#dapp`.
-
-:::
-
----
-
 ### Upgrade
 
 import Upgrade from "./cli/upgrade.md";
@@ -170,113 +170,107 @@ The CLI automatically runs in non-interactive mode if either a JUNO_TOKEN is set
 
 ---
 
-## Changes
+### Changes
 
 import Changes from "./cli/changes.md";
 
 <Changes />
 
 ---
 
-### Apply
+#### Apply
 
 import ChangesApply from "./cli/changes-apply.md";
 
 <ChangesApply />
 
 ---
 
-### List
+#### List
 
 import ChangesList from "./cli/changes-list.md";
 
 <ChangesList />
 
 ---
 
-### Reject
+#### Reject
 
 import ChangesReject from "./cli/changes-reject.md";
 
 <ChangesReject />
 
 ---
 
-## Emulator
+### Emulator
 
 import Emulator from "./cli/emulator.md";
 
 <Emulator />
 
 ---
 
-### Start
+#### Start
 
 import EmulatorStart from "./cli/emulator-start.md";
 
 <EmulatorStart />
 
 ---
 
-### Wait
+#### Wait
 
 import EmulatorWait from "./cli/emulator-wait.md";
 
 <EmulatorWait />
 
 ---
 
-## Functions
+### Functions
 
 import Functions from "./cli/functions.md";
 
 <Functions />
 
 ---
 
-## Run
-
-import Run from "./cli/run.md";
-
-<Run />
-
----
-
-### Build
+#### Build
 
 import FunctionsBuild from "./cli/functions-build.md";
 
 <FunctionsBuild />
 
 ---
 
-### Eject
+#### Eject
 
 import FunctionsEject from "./cli/functions-eject.md";
 
 <FunctionsEject />
 
 ---
 
-### Publish
+#### Publish
 
 import FunctionsPublish from "./cli/functions-publish.md";
 
 <FunctionsPublish />
 
 ---
 
-### Upgrade
+#### Upgrade
 
 import FunctionsUpgrade from "./cli/functions-upgrade.md";
 
 <FunctionsUpgrade />
 
 ---
 
-## Others
+### Run
 
-Additional commands for managing and interacting with the CLI environment.
+import Run from "./cli/run.md";
+
+<Run />
 
 ---