docs: removes code link backticks (#369)

# Motivation

<!-- Why is this change necessary? -->

# Content

<!-- Please include a summary of the change -->

# Testing

<!-- How was the change tested? -->

# Please check the following before marking your PR as ready for review

- [ ] I have added tests for my changes
- [ ] I have updated the documentation or added new documentation as
needed

Author: jayhack

.codegen/.gitignore

@@ -5,6 +5,8 @@ prompts/
 jupyter/
 .venv/
 codegen-system-prompt.txt
+*.txt
+*.pyc
 
 # Python cache files
 __pycache__/

.codegen/codemods/no_link_backticks/no_link_backticks.py

@@ -0,0 +1,43 @@
+import codegen
+from codegen import Codebase
+
+
+@codegen.function("no-link-backticks")
+def run(codebase: Codebase):
+    import re
+
+    # Define the pattern for Markdown links with backticks in the link text
+    link_pattern = re.compile(r"\[([^\]]*`[^\]]*`[^\]]*)\]\(([^)]+)\)")
+
+    # Iterate over all .mdx files in the codebase
+    for file in codebase.files(extensions=["mdx"]):
+        if file.extension == ".mdx":
+            new_content = file.content
+
+            # Find all markdown links with backticks in link text
+            matches = link_pattern.finditer(new_content)
+
+            for match in matches:
+                # Original link text with backticks
+                original_text = match.group(1)
+
+                # Remove backticks from the link text
+                new_text = original_text.replace("`", "")
+
+                # Replace the link in content
+                new_content = new_content.replace(match.group(0), f"[{new_text}]({match.group(2)})")
+
+            # Update file content if changes were made
+            if new_content != file.content:
+                file.edit(new_content)
+
+    # Commit all changes
+    codebase.commit()
+
+
+if __name__ == "__main__":
+    print("Parsing codebase...")
+    codebase = Codebase("./")
+
+    print("Running function...")
+    codegen.run(run)

docs/blog/fixing-import-loops.mdx

@@ -110,7 +110,7 @@ Not all import cycles are problematic! Some cycles using dynamic imports can wor
 
 PyTorch prevents most circular import issues through dynamic imports which can be seen through the `import_symbol.is_dynamic` property. If any edge in a strongly connected component is dynamic, runtime conflicts are typically resolved.
 
-However, we discovered an import loop worth investigating between [`flex_decoding.py`](https://github.com/pytorch/pytorch/blob/main/torch/_inductor/kernel/flex_decoding.py) and [`flex_attention.py`](https://github.com/pytorch/pytorch/blob/main/torch/_inductor/kernel/flex_attention.py):
+However, we discovered an import loop worth investigating between [flex_decoding.py](https://github.com/pytorch/pytorch/blob/main/torch/_inductor/kernel/flex_decoding.py) and [flex_attention.py](https://github.com/pytorch/pytorch/blob/main/torch/_inductor/kernel/flex_attention.py):
 
 <img src="/images/problematic-import-loop.png" alt="Invalid import loop example" />
 

docs/building-with-codegen/dependencies-and-usages.mdx

@@ -11,8 +11,8 @@ Codegen pre-computes dependencies and usages for all symbols in the codebase, en
 
 Codegen provides two main ways to track relationships between symbols:
 
-- [`.dependencies`](/api-reference/core/Symbol#dependencies) / [`.get_dependencies(...)`](/api-reference/core/Symbol#get-dependencies) - What symbols does this symbol depend on?
-- [`.usages`](/api-reference/core/Symbol#usages) / [`.usages(...)`](/api-reference/core/Symbol#usages) - Where is this symbol used?
+- [.dependencies](/api-reference/core/Symbol#dependencies) / [.get_dependencies(...)](/api-reference/core/Symbol#get-dependencies) - What symbols does this symbol depend on?
+- [.usages](/api-reference/core/Symbol#usages) / [.usages(...)](/api-reference/core/Symbol#usages) - Where is this symbol used?
 
 Dependencies and usages are inverses of each other. For example, given the following input code:
 

docs/building-with-codegen/editables-and-behaviors.mdx

@@ -11,14 +11,14 @@ This guide explains the key behaviors and how to use them effectively.
 
 ## Core Behaviors
 
-- [`HasName`](/api-reference/core/HasName): For elements with names (functions, classes, variables)
-- [`HasValue`](/api-reference/core/HasValue): For elements with values (variables, parameters)
-- [`HasBlock`](/api-reference/core/HasBlock): For elements containing code blocks (functions, classes)
-- [`Editable`](/api-reference/core/Editable): For elements that can be safely modified ([learn more](/building-with-codegen/the-editable-api))
+- [HasName](/api-reference/core/HasName): For elements with names (functions, classes, variables)
+- [HasValue](/api-reference/core/HasValue): For elements with values (variables, parameters)
+- [HasBlock](/api-reference/core/HasBlock): For elements containing code blocks (functions, classes)
+- [Editable](/api-reference/core/Editable): For elements that can be safely modified ([learn more](/building-with-codegen/the-editable-api))
 
 ## Working with Names
 
-The [`HasName`](/api-reference/core/HasName) behavior provides APIs for working with named elements:
+The [HasName](/api-reference/core/HasName) behavior provides APIs for working with named elements:
 
 ```python
 # Access the name
@@ -35,7 +35,7 @@ name_node = function.get_name()
 
 ## Working with Values
 
-The [`HasValue`](/api-reference/core/HasValue) behavior provides APIs for elements that have values:
+The [HasValue](/api-reference/core/HasValue) behavior provides APIs for elements that have values:
 
 ```python
 # Access the value
@@ -52,7 +52,7 @@ if variable.value is not None:
 
 ## Working with Code Blocks
 
-The [`HasBlock`](/api-reference/core/HasBlock) behavior provides APIs for elements containing code:
+The [HasBlock](/api-reference/core/HasBlock) behavior provides APIs for elements containing code:
 
 ```python
 # Access the code block

docs/building-with-codegen/files-and-directories.mdx

@@ -191,20 +191,20 @@ parent = dir.parent # Parent directory
 
 ## Editing Files Directly
 
-Files themselves are [`Editable`](/api-reference/core/Editable.mdx) objects, just like Functions and Classes.
+Files themselves are [Editable](/api-reference/core/Editable.mdx) objects, just like Functions and Classes.
 
 <Tip>
   Learn more about the [Editable API](/building-with-codegen/the-editable-api).
 </Tip>
 
 This means they expose many useful operations, including:
 
-- [`File.search`](/api-reference/core/File#search) - Search for all functions named "main"
-- [`File.edit`](/api-reference/core/File#edit) - Edit the file
-- [`File.replace`](/api-reference/core/File#replace) - Replace all instances of a string with another string
-- [`File.insert_before`](/api-reference/core/File#insert-before) - Insert text before a specific string
-- [`File.insert_after`](/api-reference/core/File#insert-after) - Insert text after a specific string
-- [`File.remove`](/api-reference/core/File#remove) - Remove a specific string
+- [File.search](/api-reference/core/File#search) - Search for all functions named "main"
+- [File.edit](/api-reference/core/File#edit) - Edit the file
+- [File.replace](/api-reference/core/File#replace) - Replace all instances of a string with another string
+- [File.insert_before](/api-reference/core/File#insert-before) - Insert text before a specific string
+- [File.insert_after](/api-reference/core/File#insert-after) - Insert text after a specific string
+- [File.remove](/api-reference/core/File#remove) - Remove a specific string
 
 ```python
 # Get a file
@@ -230,7 +230,7 @@ file.insert_after("def end():\npass")
 file.remove()
 ```
 
-You can frequently do bulk modifictions via the [`.edit(...)`](/api-reference/core/Editable#edit) method or [`.replace(...)`](/api-reference/core/File#replace) method.
+You can frequently do bulk modifictions via the [.edit(...)](/api-reference/core/Editable#edit) method or [.replace(...)](/api-reference/core/File#replace) method.
 
 <Note>
   Most useful operations will have bespoke APIs that handle edge cases, update
@@ -239,7 +239,7 @@ You can frequently do bulk modifictions via the [`.edit(...)`](/api-reference/co
 
 ## Moving and Renaming Files
 
-Files can be manipulated through methods like [`File.update_filepath()`](/api-reference/core/File#update-filepath), [`File.rename()`](/api-reference/core/File#rename), and [`File.remove()`](/api-reference/core/File#remove):
+Files can be manipulated through methods like [File.update_filepath()](/api-reference/core/File#update-filepath), [File.rename()](/api-reference/core/File#rename), and [File.remove()](/api-reference/core/File#remove):
 
 ```python
 # Move/rename a file
@@ -263,7 +263,7 @@ for file in codebase.files:
 
 ## Directories
 
-[`Directories`](/api-reference/core/Directory) expose a similar API to the [File](/api-reference/core/File.mdx) class, with the addition of the `subdirectories` property.
+[Directories](/api-reference/core/Directory) expose a similar API to the [File](/api-reference/core/File.mdx) class, with the addition of the `subdirectories` property.
 
 ```python
 # Get a directory

docs/building-with-codegen/git-operations.mdx

@@ -4,14 +4,14 @@ sidebarTitle: "Git Operations"
 icon: "code-branch"
 ---
 
-Many workflows require Git operations. Codegen provides a high-level API for common Git operations through the [`Codebase`](/api-reference/core/Codebase) class, including:
+Many workflows require Git operations. Codegen provides a high-level API for common Git operations through the [Codebase](/api-reference/core/Codebase) class, including:
 
-- [`Codebase.git_commit(...)`](/api-reference/core/Codebase#git_commit)
-- [`Codebase.checkout(...)`](/api-reference/core/Codebase#checkout)
+- [Codebase.git_commit(...)](/api-reference/core/Codebase#git_commit)
+- [Codebase.checkout(...)](/api-reference/core/Codebase#checkout)
 
 ## Committing Changes to Git
 
-You can commit changes to Git using the [`Codebase.git_commit(...)`](/api-reference/core/Codebase#git_commit):
+You can commit changes to Git using the [Codebase.git_commit(...)](/api-reference/core/Codebase#git_commit):
 
 ```python
 # Make some changes and call `commit()` to sync them to disk
@@ -31,8 +31,8 @@ if commit:
 
 <Note>
   `git_commit` will only commit changes that have been synced to the filesystem
-  by calling [`Codebase.commit()`](/api-reference/core/Codebase#commit). See
-  [`Commit and Reset`](/building-with-codegen/commit-and-reset) for more
+  by calling [Codebase.commit()](/api-reference/core/Codebase#commit). See
+  [Commit and Reset](/building-with-codegen/commit-and-reset) for more
   details.
 </Note>
 
@@ -53,7 +53,7 @@ if current:
 
 ## Checking Out Branches and Commits
 
-The [`Codebase.checkout(...)`](/api-reference/core/Codebase#checkout) method allows you to switch between branches and commits.
+The [Codebase.checkout(...)](/api-reference/core/Codebase#checkout) method allows you to switch between branches and commits.
 
 This will automatically re-parse the codebase to reflect the new state.
 

docs/building-with-codegen/language-support.mdx

@@ -48,15 +48,15 @@ TSCodebaseType = Codebase[
 
 Every code element has both a Python and TypeScript implementation that inherits from a common base class. For example:
 
-- [`Function`](/api-reference/core/Function)
-  - [`PyFunction`](/api-reference/python/PyFunction)
-  - [`TSFunction`](/api-reference/typescript/TSFunction)
-- [`Class`](/api-reference/core/Class)
-  - [`PyClass`](/api-reference/python/PyClass)
-  - [`TSClass`](/api-reference/typescript/TSClass)
-- [`Import`](/api-reference/core/Import)
-  - [`PyImport`](/api-reference/python/PyImport)
-  - [`TSImport`](/api-reference/typescript/TSImport)
+- [Function](/api-reference/core/Function)
+  - [PyFunction](/api-reference/python/PyFunction)
+  - [TSFunction](/api-reference/typescript/TSFunction)
+- [Class](/api-reference/core/Class)
+  - [PyClass](/api-reference/python/PyClass)
+  - [TSClass](/api-reference/typescript/TSClass)
+- [Import](/api-reference/core/Import)
+  - [PyImport](/api-reference/python/PyImport)
+  - [TSImport](/api-reference/typescript/TSImport)
 
 ...
 
@@ -91,8 +91,8 @@ for function in codebase.functions:
 
 Some features are only available in TypeScript codebases:
 
-- **Types and Interfaces**: TypeScript's rich type system ([`TSTypeAlias`](/api-reference/typescript/TSTypeAlias), [`TSInterface`](/api-reference/typescript/TSInterface))
-- **Exports**: Module exports and re-exports ([`TSExport`](/api-reference/typescript/TSExport))
+- **Types and Interfaces**: TypeScript's rich type system ([TSTypeAlias](/api-reference/typescript/TSTypeAlias), [TSInterface](/api-reference/typescript/TSInterface))
+- **Exports**: Module exports and re-exports ([TSExport](/api-reference/typescript/TSExport))
 - **JSX/TSX**: React component handling (see [React and JSX](/building-with-codegen/react-and-jsx))
 
 Example of TypeScript-specific features:

docs/building-with-codegen/moving-symbols.mdx

@@ -7,11 +7,11 @@ iconType: "solid"
 
 Codegen provides fast, configurable and safe APIs for moving symbols (functions, classes, variables) between files while automatically handling imports and dependencies.
 
-The key API is [`Symbol.move_to_file(...)`](/api-reference/core/Symbol#move-to-file).
+The key API is [Symbol.move_to_file(...)](/api-reference/core/Symbol#move-to-file).
 
 ## Basic Symbol Movement
 
-Simply call [`Symbol.move_to_file(...)`](/api-reference/core/Symbol#move-to-file) to move a symbol to a new file.
+Simply call [Symbol.move_to_file(...)](/api-reference/core/Symbol#move-to-file) to move a symbol to a new file.
 
 ```python
 # Manipulation code:
@@ -35,7 +35,7 @@ helper_func.move_to_file(file2)
 
 ## Moving Strategies
 
-The [`Symbol.move_to_file(...)`](/api-reference/core/Symbol#move-to-file) method accepts a `strategy` parameter, which can be used to control how imports are updated.
+The [Symbol.move_to_file(...)](/api-reference/core/Symbol#move-to-file) method accepts a `strategy` parameter, which can be used to control how imports are updated.
 
 Your options are:
 
@@ -51,7 +51,7 @@ Your options are:
 
 ## Moving Symbols in Bulk
 
-Make sure to call [`Codebase.commit(...)`](/api-reference/core/Codebase#commit) _after_ moving symbols in bulk for performant symbol movement.
+Make sure to call [Codebase.commit(...)](/api-reference/core/Codebase#commit) _after_ moving symbols in bulk for performant symbol movement.
 
 ```python
 # Move all functions with a specific prefix

docs/building-with-codegen/type-annotations.mdx

@@ -158,7 +158,7 @@ function.set_return_type("List[str]")
 
 ### Type Resolution
 
-Type resolution uses [`Type.resolved_value`](/api-reference/core/Type#resolved-value) to get the actual symbols that a type refers to:
+Type resolution uses [Type.resolved_value](/api-reference/core/Type#resolved-value) to get the actual symbols that a type refers to:
 
 ```python
 # Get the actual symbols for a type

docs/introduction/work-with-ai.mdx

@@ -25,7 +25,7 @@ import {
 
 The [Codegen CLI](/cli/about) provides commands to generate `.md` files that can be fed to any AI assistant for more accurate and contextual help.
 
-When you create a new codemod via [`codegen create`](/cli/create):
+When you create a new codemod via [codegen create](/cli/create):
 
 ```bash
 codegen create delete-dead-imports --description "Delete unused imports"
@@ -41,7 +41,7 @@ You can find this generated prompt in the `.codegen/prompts/<codemod-name>-syste
 
 <Note>
   All contents of the `.codegen/prompts` directory are by default ignored the
-  `.gitignore` file. after running [`codegen init`](/cli/init)
+  `.gitignore` file. after running [codegen init](/cli/init)
 </Note>
 
 This `.md` file can be used with any AI assistant (Claude, GPT-4, etc.) to get more accurate and contextual help.
@@ -50,7 +50,7 @@ This `.md` file can be used with any AI assistant (Claude, GPT-4, etc.) to get m
 
 <Steps>
   <Step title="Create a codemod with description">
-    Use the [`create` command](/cli/create) with a detailed description of what you want to accomplish:
+    Use the [create command](/cli/create) with a detailed description of what you want to accomplish:
     ```bash
     codegen create modernize-components --description "Convert class components to functional components with hooks"
     ```

docs/tutorials/creating-documentation.mdx

@@ -8,8 +8,8 @@ iconType: "solid"
 This guide demonstrates how to determine docs coverage and create documentation for your codebase.
 
 This primarily leverages two APIs:
-- [`codebase.ai(...)`](/api-reference/core/Codebase#ai) for generating docstrings
-- [`function.set_docstring(...)`](/api-reference/core/HasBlock#set-docstring) for modifying them
+- [codebase.ai(...)](/api-reference/core/Codebase#ai) for generating docstrings
+- [function.set_docstring(...)](/api-reference/core/HasBlock#set-docstring) for modifying them
 
 ## Determining Documentation Coverage
 
@@ -74,7 +74,7 @@ Which provides the following output:
 
 To identify areas of low documentation coverage, you can iterate through all directories and count the number of functions with docstrings.
 
-<Note>Learn more about [`Directories` here](/building-with-codegen/files-and-directories).</Note>
+<Note>Learn more about [Directories here](/building-with-codegen/files-and-directories).</Note>
 
 ```python python
 # Track directory stats

src/codegen/cli/workspace/initialize_workspace.py

@@ -147,6 +147,8 @@ def modify_gitignore(codegen_folder: Path):
         "__pycache__/",
         "*.py[cod]",
         "*$py.class",
+        "*.txt",
+        "*.pyc",
         "",
         "# Keep config.toml and codemods",
         "!config.toml",