docs: deprecation warnings for clarinet test and clarinet run (#1157)

* docs: deprecation warning for clarinet test and clarinet run

* docs: fix typo

* docs: typo

README.md

@@ -351,6 +351,8 @@ This annotation tells the check-checker to consider the specified variables to b
 
 ### Execute a test suite
 
+> Warning: `clarinet test` will soon be deprecated in favor of a new way of testing smart contracts. The new documentation is under construction. In the meantime, learn more [in the clarinet-sdk Readme](https://github.com/hirosystems/clarinet/blob/01da3550670f321a2f19fd3b0f8df0fb4b769b08/components/clarinet-sdk/README.md).
+
 Clarinet provides a testing harness based on Deno that can enable you to create automated unit tests or pseudo-integration tests using Typescript.
 
 ```bash
@@ -396,10 +398,10 @@ open coverage/index.html
 Clarinet can also be used to optimize costs. When executing a test suite, Clarinet will keep track of all the costs being computed when executing the `contract-call`, and display the most expensive ones in a table:
 
 ```bash
-clarinet test --cost
+clarinet test --costs
 ```
 
-The `--cost` option can be used in conjunction with `--watch` and filters to maximize productivity, as illustrated here:
+The `--costs` option can be used in conjunction with `--watch` and filters to maximize productivity, as illustrated here:
 
 ![costs](docs/images/costs.gif)
 
@@ -601,27 +603,6 @@ You may also add the steps above in your existing workflows. The generated code
 
 For more information on how you can use GitHub Actions with Clarinet, please see the [A Simple CI With Clarinet and GitHub](https://www.youtube.com/watch?v=cEv6Mi4EcKQ&list=PL5Ujm489LoJaAz9kUJm8lYUWdGJ2AnQTb&index=8) YouTube video
 
-### Extensions
-
-Clarinet can easily be extended by community members: open source contributions to Clarinet are welcome, but you may also write your own Clarinet extensions if you want to integrate Clarity contracts with your own tooling and workflow.
-
-| Name                      | wallet access | disk write | disk read | Deployment                                                            | Description                                                                                                                                       |
-| ------------------------- | ------------- | ---------- | --------- | --------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- |
-| stacksjs-helper-generator | no            | yes        | no        | https://deno.land/x/[email protected]/ext/stacksjs-helper-generator.ts | Facilitates contract integration by generating some typescript constants that can be used with stacks.js. Never hard code a stacks address again! |
-|                           |               |            |           |                                                                       |
-
-#### How to use extensions
-
-Extensions are run with the following syntax:
-
-```
-clarinet run --allow-write https://deno.land/x/[email protected]/ext/stacksjs-helper-generator.ts
-```
-
-An extension can be deployed as a standalone plugin on Deno, or may also be a local file if it includes sensitive / private setup informations.
-
-As illustrated in the example above, permissions (wallet / disk read / disk write) are declared using command flags. If at runtime, the Clarinet extension is trying to write to disk, read disk, or access wallets without permission, the script will fail.
-
 ### Debug your contracts
 
 #### VS Code Debugger

docs/feature-guides/extend-clarinet.md

@@ -2,6 +2,8 @@
 title: Extend Clarinet
 ---
 
+> Warning: `clarinet run` will soon be deprecated in favor of a new way of interacting with smart contracts. The new documentation is under construction. In the meantime, learn more [in the clarinet-sdk Readme](https://github.com/hirosystems/clarinet/blob/01da3550670f321a2f19fd3b0f8df0fb4b769b08/components/clarinet-sdk/README.md).
+
 Extend Clarinet to integrate clarity contracts with your own tooling and workflow.
 
 *Topics covered in this guide*:

docs/how-to-guides/how-to-test-contract.md

@@ -2,16 +2,19 @@
 title: Test Contract
 ---
 
+> Warning: `clarinet test` will soon be deprecated in favor of a new way of testing smart contracts. The new documentation is under construction. In the meantime, learn more [in the clarinet-sdk Readme](https://github.com/hirosystems/clarinet/blob/01da3550670f321a2f19fd3b0f8df0fb4b769b08/components/clarinet-sdk/README.md).
+
 Clarinet supports automatic testing, where your blockchain application requirements can be converted to test cases. Clarinet comes with a testing harness based on Deno that applies the unit tests you write in TypeScript to your smart contracts.
 
 *Topics covered in this guide*:
 
-* [Instructions to write unit tests](#clarity-contracts-and-unit-tests)
-* [Increase test coverage](#measure-and-increase-code-coverage)
-* [Clarinet usage to optimize costs](#cost-optimization)
-* [Clarity REPL console](#load-contracts-in-a-console)
-* [Interact with contracts on mainnet](#interacting-with-contracts-deployed-on-mainnet)
-* [Clarinet usage in Github actions](#use-clarinet-in-your-ci-workflow-as-a-github-action)
+- [Clarity contracts and unit tests](#clarity-contracts-and-unit-tests)
+- [Measure and increase code coverage](#measure-and-increase-code-coverage)
+- [Cost optimization](#cost-optimization)
+- [Load contracts in a console](#load-contracts-in-a-console)
+- [Spawn a local Devnet](#spawn-a-local-devnet)
+- [Interacting with contracts other contracts](#interacting-with-contracts-other-contracts)
+- [Use Clarinet in your CI workflow as a GitHub Action](#use-clarinet-in-your-ci-workflow-as-a-github-action)
 
 ## Clarity contracts and unit tests
 
@@ -39,7 +42,7 @@ Let us consider a `counter` smart contract to understand how to write unit tests
 
 Our `counter` application keeps track of an initialized value, allows for incrementing and decrementing, and prints actions as a log. Let us turn these requirements into unit tests.
 
-### Unit tests for `counter` example
+### Unit tests for `counter` example  <!-- omit from toc -->
 
 When you created your Clarity contract with `clarinet contract new <my-project>`, Clarinet automatically created a test file for the contract within the tests directory:  `tests/my-projects_test.ts`. Other files under the `tests/` directory following the Deno test naming convention will also be included:
 
@@ -98,7 +101,7 @@ For a complete list of classes, objects, and interfaces available, see [Deno's C
 You can watch a step-by-step walkthrough of using `clarinet test` and watch [Executing Tests and Checking Code Coverage](https://www.youtube.com/watch?v=j2TZ560xEPA&list=PL5Ujm489LoJaAz9kUJm8lYUWdGJ2AnQTb&index=10).
 
 
-### Comprehensive unit tests for `counter`
+### Comprehensive unit tests for `counter`  <!-- omit from toc -->
 
 Let us now write a higher coverage test suite.
 
@@ -192,10 +195,10 @@ open coverage/index.html
 Clarinet can also be used for optimizing costs. When you execute a test suite, Clarinet keeps track of all costs being computed when executing the `contract-call`, and display the most expensive ones in a table:
 
 ```bash
-clarinet test --cost
+clarinet test --costs
 ```
 
-The `--cost` option can be used in conjunction with `--watch` and filters to maximize productivity, as illustrated here:
+The `--costs` option can be used in conjunction with `--watch` and filters to maximize productivity, as illustrated here:
 
 ![costs](../images//costs.gif)
 
@@ -227,7 +230,9 @@ clarinet integrate
 
 Make sure that you have a working installation of Docker running locally.
 
-## Interacting with contracts deployed on Mainnet
+## Interacting with contracts
+
+### Deployed on Mainnet <!-- omit from toc -->
 
 Composition and interactions between protocols and contracts are one of the key innovations in blockchains. 
 Clarinet was designed to handle these types of interactions.
@@ -255,9 +260,9 @@ As a step-by-step example, we use here the following contract, [**bitcoin-whales
 
 If you examine this contract, you will see that there are 3 different dependencies: two from the **same** project (included in the same `Clarinet.toml` file), and one referring to a contract deployed outside of the current project.
 
-## Same Project
+### Same Project <!-- omit from toc -->
 
-In the contract snippet below *(line:260-265)*, there are dependencies on the contracts conversion and conversion-v2 which are included in the same `Clarinet.toml` file.
+In the contract snippet below, there are dependencies on the contracts conversion and conversion-v2 which are included in the same `Clarinet.toml` file.
 
 ```clarity
 (define-read-only (get-token-uri (token-id uint))
@@ -268,9 +273,9 @@ In the contract snippet below *(line:260-265)*, there are dependencies on the co
 )
 ```
 
-## External Deployer 
+### External Deployer <!-- omit from toc -->
 
-In this snippet, there is a dependency on the `nft-trait` *(line:001)* deployed by `'SP2PABAF9FTAJYNFZH93XENAJ8FVY99RRM50D2JG9`.
+In this snippet, there is a dependency on the `nft-trait` deployed by `'SP2PABAF9FTAJYNFZH93XENAJ8FVY99RRM50D2JG9`.
 
 ```clarity
 (impl-trait 'SP2PABAF9FTAJYNFZH93XENAJ8FVY99RRM50D2JG9.nft-trait.nft-trait)