### Setup sem

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Commands to set up sem for the first time, including creating a wrapper script, setting git config, and installing a pre-commit hook.

```bash
sem setup
✓ Created wrapper script
✓ Set git config --global diff.external = sem
✓ Pre-commit hook installed
```

--------------------------------

### Installation

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Install sem using npm.

```bash
npm install -g sem
```

--------------------------------

### Command Examples

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Various command examples for sem, showcasing different functionalities.

```bash
sem config set theme.dark
sem config get theme
sem --help
sem --version
```

--------------------------------

### sem context example

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Example output of the `sem context` command.

```text
sem context

Smart context for AI. Token-budgeted context window: the entity, its dependencies, and dependents. Fits in any LLM prompt.

context for authenticateUser (budget: 8000)
  target:          ~705 tokens
  dependencies:    ~256 tokens
  dependents:      ~812 tokens
```

--------------------------------

### sem log example

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Example output of the `sem log` command.

```text
sem log

How did it evolve? Git history for a single entity. See every commit that touched a specific function.

│  ae576ab  Rohan  02-05  added
│  a105183  Rohan  02-08  modified (logic)
│  a1a6fbf  Rohan  04-03  modified (logic)
```

--------------------------------

### sem blame example

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Example output of the `sem blame` command.

```text
sem blame

│  ⊕ render_inline_diff  a1a6fbf  Rohan  04-03
│  ⊕ format_terminal     a1a6fbf  Rohan  04-03
```

--------------------------------

### sem entities example

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Example output of the `sem entities` command.

```text
sem entities

What's under a path? Lists every function, class, method, and type with line ranges.

entities: src/auth/login.ts
  function validateToken     (L12:24)
  function authenticateUser  (L26:45)
  interface AuthConfig       (L47:52)
```

--------------------------------

### sem impact example

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Example output of the `sem impact` command.

```text
sem impact

What breaks? Cross-file dependency graph shows every entity that depends on a given function, plus affected tests.

⊕ function authenticateUser
  → depends on:  db.findUser, rateLimiter
  ← used by:    loginRoute, authMiddleware
  ! 42 entities transitively affected
```

--------------------------------

### Install with Homebrew

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/llms.txt

Installs the sem CLI using the Homebrew package manager.

```bash
brew install sem-cli
```

--------------------------------

### sem command example with flags

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/details.html

Shows an example of using a specific sem command with its associated flags.

```bash
sem build --target=release --jobs=4
```

--------------------------------

### Git Diff Example

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Demonstrates how sem can display git diffs with syntax highlighting.

```diff
git diff --color=always | sem diff
```

--------------------------------

### MCP server and sem setup

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/changelog.html

Details about the new `sem-mcp` crate, MCP tools, and `sem setup` command.

```text
New `sem-mcp` crate: an MCP server exposing 6 tools (`sem_entities`, `sem_diff`, `sem_blame`, `sem_impact`, `sem_log`, `sem_context`) for AI agent integration. New `sem setup` command replaces `git diff` globally and installs a pre-commit hook showing entity-level blast radius. `sem unsetup` to revert.
```

--------------------------------

### Basic Usage

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Example of using sem to list files with colorized output.

```bash
sem ls -l --color=auto
```

--------------------------------

### Install MCP Binary

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Command to install the MCP binary from the local sem/crates directory.

```bash
cd sem/crates
cargo install --path sem-mcp
```

--------------------------------

### Install sem-core and sem-cli

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/changelog.html

Instructions for installing the sem-core and sem-cli packages via Cargo or Homebrew.

```bash
brew install sem-cli
# or

```

```bash
cargo install sem-cli
```

--------------------------------

### Install sem using npm

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Installs the sem npm wrapper as a development dependency.

```bash
npm install --save-dev @ataraxy-labs/sem
```

--------------------------------

### Example Usage of sem command

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/details.html

Demonstrates a typical command-line interaction with the 'sem' tool, showing its output and structure.

```bash
sem --help
sem --version
sem --config path/to/config.yaml
sem --output path/to/output.json
sem --verbose
sem --quiet
sem --log path/to/log.txt
sem --no-color
sem --force
sem --yes
sem --no
sem --dry-run
sem --debug
sem --trace
sem --help <command>
sem <command> --help
```

--------------------------------

### JSON Output Example

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/llms.txt

Example of the JSON output format when using the 'sem diff --format json' command.

```bash
sem diff --format json
```

```json
{
  "summary": { "fileCount": 2, "added": 1, "modified": 1, "deleted": 1, "total": 3 },
  "changes": [
    {
      "entityId": "src/auth.ts::function::validateToken",
      "changeType": "added",
      "entityType": "function",
      "entityName": "validateToken",
      "filePath": "src/auth.ts"
    }
  ]
}
```

--------------------------------

### Install sem using Bun

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Adds the sem package using Bun and trusts it to allow the postinstall script to download the binary.

```bash
bun add -d @ataraxy-labs/sem
bun pm trust @ataraxy-labs/sem
```

--------------------------------

### sem diff command syntax examples

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/changelog.html

Examples demonstrating the full git diff syntax support in `sem diff`, including single ref, two-dot range, three-dot merge-base, pathspec filtering, and `--cached`.

```bash
sem diff HEAD~3
sem diff main..feature
sem diff main...feature
sem diff -- src/
sem diff --cached
```

--------------------------------

### sem diff markdown output example

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/changelog.html

Example of using `sem diff --format markdown` to render entity changes as markdown tables.

```bash
sem diff --format markdown
```

--------------------------------

### sem log command example

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/changelog.html

Example of using the `sem log` command to trace an entity through git history. Supports `--verbose` for diffs and `--json` for machine output.

```bash
sem log <entity>
```

--------------------------------

### sem command example with output redirection

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/details.html

Demonstrates how to redirect the output of a sem command to a JSON file.

```bash
sem build --output=build/output.json
```

--------------------------------

### Custom extensions and extensionless files

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Example of custom extensions mapping in a .semrc file.

```bash
.xyz = cpp
.j = json
.mypy = python
```

--------------------------------

### sem diff verbose output example

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/changelog.html

Example of using `sem diff -v` to show inline before/after content for modified entities.

```bash
sem diff -v
```

--------------------------------

### Build sem from source

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Builds and installs the sem CLI from its source code repository, requiring Rust.

```bash
cargo install --git https://github.com/Ataraxy-Labs/sem sem-cli
```

--------------------------------

### Register file extensions for the new language

Source: https://github.com/ataraxy-labs/sem/blob/main/CONTRIBUTING.md

Example of how to add the file extensions for the new language to the EXTENSIONS array in Rust.

```rust
static EXTENSIONS: &[&str] = &[
    // ... existing extensions ...
    ".scala", ".sc",
];
```

--------------------------------

### Register the new LanguageConfig in ALL_CONFIGS

Source: https://github.com/ataraxy-labs/sem/blob/main/CONTRIBUTING.md

Example of how to add the new language configuration to the static ALL_CONFIGS array in Rust.

```rust
static ALL_CONFIGS: &[&LanguageConfig] = &[
    // ... existing configs ...
    &SCALA_CONFIG,
];
```

--------------------------------

### JSON Diff Output

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Example JSON output for the 'sem diff' command.

```json
{
  "summary": {
    "fileCount": 2,
    "added": 1,
    "modified": 1,
    "deleted": 1,
    "total": 3
  },
  "changes": [
    {
      "entityId": "src/auth.ts::function::validateToken",
      "changeType": "added",
      "entityType": "function",
      "entityName": "validateToken",
      "filePath": "src/auth.ts"
    }
  ]
}
```

--------------------------------

### sem diff command

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/details.html

Example of using the sem diff command with JSON output.

```bash
sem diff --format json | jq
```

--------------------------------

### Add tree-sitter dependency to Cargo.toml

Source: https://github.com/ataraxy-labs/sem/blob/main/CONTRIBUTING.md

Example of how to add a tree-sitter grammar dependency to the project's Cargo.toml file.

```toml
[dependencies]
tree-sitter-scala = "0.23"
```

--------------------------------

### Elixir example for call_entity_identifiers

Source: https://github.com/ataraxy-labs/sem/blob/main/CONTRIBUTING.md

Illustrates how Elixir uses function calls for entity definitions, requiring `call_entity_identifiers`.

```elixir
defmodule MyApp do    # "defmodule" is a call, not a keyword
  def greet(name) do  # "def" is a call
    "Hello #{name}"
  end
end
```

--------------------------------

### Node.js vs Rust Performance Breakdown

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/changelog.html

A comparison of the time taken for initial setup and execution between Node.js and Rust for a specific task, highlighting the performance advantages of Rust.

```text
Node.js breakdown: ~120ms V8 startup, ~80ms module resolution, ~50ms WASM grammar load, ~40ms git subprocess spawn.
Rust breakdown: ~3ms binary load, ~5ms git2 repo open, ~17ms parse + match.
```

--------------------------------

### sem diff commands

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/llms.txt

Examples of using the 'sem diff' command for various use cases, including comparing working changes, staged changes, specific commits, commit ranges, individual files, and different output formats.

```bash
sem diff                          # working changes
sem diff --staged                 # staged only
sem diff --commit abc1234         # specific commit
sem diff --from HEAD~5 --to HEAD  # commit range
sem diff file1.ts file2.ts       # compare two files (no git needed)
sem diff --format json            # JSON output for agents/CI
sem diff --format plain           # git-status style
sem diff --format markdown        # markdown tables
sem diff --stdin --format json    # read file changes from stdin
sem diff --file-exts .py .rs      # filter by extension
sem diff -v                       # verbose inline content diffs
```

--------------------------------

### sem blame

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Get blame information for a file, outputting in JSON format.

```bash
sem blame src/auth.ts --json
```

--------------------------------

### sem graph commands

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/llms.txt

Examples of using the 'sem graph' command to generate a cross-file entity dependency graph, with options to filter by entity, file extensions, and output format.

```bash
sem graph
sem graph --entity validateToken
sem graph --file-exts .py
sem graph --format json
```

--------------------------------

### Add a getter function for tree-sitter Language

Source: https://github.com/ataraxy-labs/sem/blob/main/CONTRIBUTING.md

Example Rust function to return the tree-sitter Language for a specific grammar, demonstrating common patterns.

```rust
fn get_scala() -> Option<Language> {
    Some(tree_sitter_scala::LANGUAGE.into())
}
```

--------------------------------

### sem blame commands

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/llms.txt

Examples of using the 'sem blame' command to show entity-level blame information for a given file, with an option for JSON output.

```bash
sem blame src/auth.ts
sem blame src/auth.ts --json
```

--------------------------------

### Filter analysis by file extensions

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/changelog.html

Example of using the --file-exts flag to scope analysis to specific file types, such as Python files.

```bash
sem diff --file-exts .py
```

--------------------------------

### sem impact commands

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/llms.txt

Examples of using the 'sem impact' command for transitive impact analysis, showing what else is affected if a specific entity changes, with options for JSON output and filtering by file extensions.

```bash
sem impact validateToken
sem impact validateToken --json
sem impact validateToken --file-exts .py
```

--------------------------------

### Full impact analysis with sem impact

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Performs a full impact analysis starting from a given entity.

```bash
sem impact authenticateUser
```

--------------------------------

### Word-level inline diffs

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/changelog.html

Example of using `sem diff --verbose` to highlight word-level changes within lines.

```bash
sem diff --verbose
```

--------------------------------

### Define the LanguageConfig for a new language

Source: https://github.com/ataraxy-labs/sem/blob/main/CONTRIBUTING.md

Example static LanguageConfig struct definition in Rust for Scala, specifying entity types, extensions, and the getter function.

```rust
static SCALA_CONFIG: LanguageConfig = LanguageConfig {
    id: "scala",
    extensions: &[".scala", ".sc"],
    entity_node_types: &[
        "function_definition",
        "class_definition",
        "object_definition",
        "trait_definition",
        "val_definition",
        "var_definition",
        "type_definition",
    ],
    container_node_types: &["template_body", "block"],
    call_entity_identifiers: &[],
    suppressed_nested_entities: &[],
    get_language: get_scala,
};
```

--------------------------------

### Add a test for entity extraction of the new language

Source: https://github.com/ataraxy-labs/sem/blob/main/CONTRIBUTING.md

Example Rust test case to verify entity extraction for Scala code, including assertions on extracted entity names.

```rust
#[test]
fn test_scala_entity_extraction() {
    let code = r#"#
class UserService {
  def getUsers(): List[User] = {
    db.findAll()
  }
}

object AppConfig {
  val version = "1.0"
}

trait Repository[T] {
  def findById(id: String): Option[T]
}
"#;
    let plugin = CodeParserPlugin;
    let entities = plugin.extract_entities(code, "UserService.scala");
    let names: Vec<&str> = entities.iter().map(|e| e.name.as_str()).collect();
    eprintln!("Scala entities: {:?}", entities.iter().map(|e| (&e.name, &e.entity_type)).collect::<Vec<_>>());

    assert!(names.contains(&"UserService"), "got: {:?}", names);
    assert!(names.contains(&"AppConfig"), "got: {:?}", names);
    assert!(names.contains(&"Repository"), "got: {:?}", names);
}
```

--------------------------------

### Use as default Git diff

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Replace `git diff` output with entity-level diffs. Agents and humans get sem output automatically without changing any commands.

```bash
sem setup
```

--------------------------------

### suppressed_nested_entities Example

Source: https://github.com/ataraxy-labs/sem/blob/main/CONTRIBUTING.md

Example of how to configure suppressed_nested_entities to prevent double-extraction of child entities within parent entities.

```rust
suppressed_nested_entities: &[SuppressedNestedEntity {
    parent_entity_node_type: "block",
    child_entity_node_type: "attribute",
}],
```

--------------------------------

### Build

Source: https://github.com/ataraxy-labs/sem/blob/main/crates/README.md

Instructions to build the project in release mode.

```bash
cargo build --release
# Binary at target/release/sem
```

--------------------------------

### Build and Test

Source: https://github.com/ataraxy-labs/sem/blob/main/SKILL.md

Commands to build the CLI binary and run tests for the sem project.

```bash
cargo build --release -p sem-cli     # binary at target/release/sem
cargo test --workspace               # 134 tests
```

--------------------------------

### Build from source

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/llms.txt

Clones the sem repository and builds the CLI from source using Cargo.

```bash
git clone https://github.com/Ataraxy-Labs/sem
cd sem/crates && cargo install --path sem-cli
```

--------------------------------

### sem command structure

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/details.html

Illustrates the general structure of a sem command, including global flags and command-specific arguments.

```bash
sem [global flags] <command> [command flags]
```

--------------------------------

### Run sem using Docker

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Builds a Docker image for sem and runs a container to perform a diff operation within a mounted repository.

```bash
docker build -t sem .
docker run --rm -it -u "$(id -u):$(id -g)" -v "$(pwd):/repo" sem diff
```

--------------------------------

### Tests

Source: https://github.com/ataraxy-labs/sem/blob/main/crates/README.md

Command to run tests and the number of tests.

```bash
cargo test
# 134 tests
```

--------------------------------

### Consolidated Commands and MCP Tools

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/changelog.html

Explanation of command consolidation and MCP tool reduction.

```text
Removed redundant CLI commands (`status`, `watch`, `review`, `comment`, `label`, `history`). Final 6: `diff`, `impact`, `blame`, `log`, `entities`, `context`. MCP server trimmed from 9 to 6 tools: one tool per CLI command. Do fewer things, do them well.
```

--------------------------------

### sem entities

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

List all entities under a file or directory path.

```bash
sem entities
```

```bash
sem entities .
```

```bash
sem entities src/auth.ts
```

```bash
# JSON output
sem entities --json
```

```bash
sem entities src/auth.ts --json
```

--------------------------------

### MCP Server Configuration

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Configuration for the MCP server, specifying the command to run.

```json
{
  "mcpServers": {
    "sem": {
      "command": "sem-mcp"
    }
  }
}
```

--------------------------------

### Run tests command

Source: https://github.com/ataraxy-labs/sem/blob/main/CONTRIBUTING.md

Command to navigate to the crates directory and run all tests.

```bash
cd crates && cargo test
```

--------------------------------

### Commands

Source: https://github.com/ataraxy-labs/sem/blob/main/crates/README.md

Common commands for the sem CLI, including entity-level diff, blame, graph, and impact analysis, with options for filtering by file extensions.

```bash
# Entity-level diff
sem diff

# Entity-level blame (who last touched each function/class)
sem blame src/auth.ts

# Cross-file dependency graph
sem graph

# Impact analysis (if this entity changes, what else is affected?)
sem impact validateToken

# Filter to specific languages in a multi-language repo
sem graph --file-exts .py
sem diff --file-exts .py .rs
sem impact validateToken --file-exts .py
```

--------------------------------

### sem log

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Track how a single entity evolved through git history.

```bash
sem log authenticateUser
```

```bash
# Verbose mode (show content diff between versions)
sem log authenticateUser -v
```

```bash
# Limit commits scanned
sem log authenticateUser --limit 20
```

```bash
# JSON output
sem log authenticateUser --json
```

--------------------------------

### Graph Caching Performance

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/benchmarks.html

Compares the time taken for 5 graph calls with and without caching.

```text
5 graph calls
no caching (separate processes)

5 graph calls
in one session (memory cache)
```

--------------------------------

### Plain text output for semantic diff

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Formats the semantic diff output in a plain text style, similar to `git status`.

```bash
sem diff --format plain
```

--------------------------------

### Architecture

Source: https://github.com/ataraxy-labs/sem/blob/main/crates/README.md

The project is structured as a Cargo workspace with two main crates: sem-core (library) and sem-cli (binary).

```text
sem-core/    # Library: entity extraction, structural hashing, semantic diff,
             # dependency graph, impact analysis, git bridge
sem-cli/     # Binary: diff, blame, graph, impact commands
```

--------------------------------

### Rust Library Dependency

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/llms.txt

How to include 'sem-core' as a Rust library dependency in your project.

```toml
[dependencies]
sem-core = { git = "https://github.com/Ataraxy-Labs/sem", version = "0.3" }
```

--------------------------------

### sem context

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Token-budgeted context for LLMs: the entity, its dependencies, and its dependents, fitted to a token budget.

```bash
sem context authenticateUser
```

```bash
# Custom token budget
sem context authenticateUser --budget 4000
```

```bash
# JSON output
sem context authenticateUser --json
```

--------------------------------

### Git diff vs Sem diff

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Compares the output of git diff with sem diff for a specific file.

```diff
git diff

diff --git a/src/auth/login.ts b/src/auth/login.ts
index 4a2b1c0..8f3d2e1 100644
---	 a/src/auth/login.ts
+++ b/src/auth/login.ts
@@ -12,6 +12,18 @@
+export function validateToken(token: string) {
+	const decoded = jwt.verify(token, SECRET);
+	if (!decoded.exp || decoded.exp < Date.now()) {
+		throw new TokenExpiredError();
+	}
+	return decoded;
+}
+
@@ -24,8 +36,10 @@
 export async function authenticateUser(
-  const user = await db.findUser(email);
-  if (!user) return null;
+	const user = await db.findUser(email);
+	if (!user) throw new UserNotFoundError();
+	await rateLimiter.check(email);
@@ -45,12 +59,0 @@
-export function legacyAuth(user, pass) {
-	return db.query('SELECT * FROM users
-	  WHERE email = ? AND password = ?',
-	  [user, pass]);
-}

sem diff

┌─ src/auth/login.ts ────────────────
│
│  ⊕ function  validateToken    [added]
│  ∆ function  authenticateUser [modified]
│  ⊖ function  legacyAuth       [deleted]
│
└────────────────────────────────────

3 entities changed across 1 file
```

--------------------------------

### Rust Library Dependency

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Adding sem-core as a Rust library dependency in Cargo.toml.

```toml
[dependencies]
sem-core = { git = "https://github.com/Ataraxy-Labs/sem", version = "0.5" }
```

--------------------------------

### Quick fix for GNU Parallel name conflict (Homebrew PATH)

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Ensures the Homebrew bin directory is prioritized in the PATH to resolve potential name conflicts with GNU Parallel.

```bash
# Option 3: if installed via Homebrew
export PATH="$(brew --prefix)/bin:$PATH"
```

--------------------------------

### JSON output for semantic diff

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Formats the semantic diff output as JSON, suitable for programmatic use by AI agents or CI pipelines.

```bash
sem diff --format json
```

--------------------------------

### Direct dependencies analysis with sem impact

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Shows only the direct dependencies of a given entity using `sem impact`.

```bash
sem impact authenticateUser --deps
```

--------------------------------

### Impact Analysis Comparison

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/benchmarks.html

Compares the number of entities found by `grep` versus `sem_impact` for transitive dependencies.

```bash
grep EntityGraph
string matches (imports, comments, type annotations)

sem_impact
entities in the transitive dependency chain
```

--------------------------------

### Compare any two files with sem diff

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Compares two arbitrary files using semantic diff, even outside of a Git repository.

```bash
sem diff file1.ts file2.ts
```

--------------------------------

### Quick fix for GNU Parallel name conflict (alias)

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Sets up a shell alias to ensure the correct sem binary is used when there's a name conflict with GNU Parallel.

```bash
# Option 1: alias in your shell profile (~/.bashrc, ~/.zshrc)
alias sem="$HOME/.cargo/bin/sem"
```

--------------------------------

### tree-sitter parse command

Source: https://github.com/ataraxy-labs/sem/blob/main/CONTRIBUTING.md

Command to parse a file using tree-sitter and print the full AST with node types.

```bash
tree-sitter parse sample.scala
```

--------------------------------

### Test Targeting Comparison

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/benchmarks.html

Compares the number of tests to run with `cargo test` versus `sem_impact(mode="tests")`.

```bash
cargo test
run everything

sem_impact(mode="tests")
tests that actually depend on EntityGraph
```

--------------------------------

### Hero Terminal Animation - sem diff

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/index.html

Simulates the output of the 'sem diff' command in a terminal, showing changes in files.

```javascript
function copyCmd(el) { navigator.clipboard.writeText('brew install sem-cli'); let copied = el.querySelector('.copied'); if (copied) { copied.classList.add('show'); setTimeout(() => copied.classList.remove('show'), 1500); } }
// Hero terminal typing animation
(function() {
  const el = document.getElementById('hero-terminal');
  if (!el) return;
  const lines = [
    // --- sem diff ---
    { text: '$ sem diff', cls: 'cmd', pause: 500, typing: true },
    { text: '', pause: 300 },
    { text: '┌─ src/auth/login.ts ──────────────────────────────────', cls: 'd', pause: 50 },
    { text: '│', cls: 'd', pause: 30 },
    { parts: [
        { text: '│ ', cls: 'd' },
        { text: '⊕', cls: 'g' },
        { text: ' function ', cls: 'd' },
        { text: 'validateToken', cls: 'w' },
        { text: ' ', cls: '' },
        { text: ' [added]', cls: 'g' },
      ], pause: 80 },
    { parts: [
        { text: '│ ', cls: 'd' },
        { text: '∆', cls: 'y' },
        { text: ' function ', cls: 'd' },
        { text: 'authenticateUser', cls: 'w' },
        { text: ' ', cls: '' },
        { text: ' [modified]', cls: 'y' },
      ], pause: 80 },
    { parts: [
        { text: '│ ', cls: 'd' },
        { text: '⊖', cls: 'r' },
        { text: ' function ', cls: 'd' },
        { text: 'legacyAuth', cls: 'w' },
        { text: ' ', cls: '' },
        { text: ' [deleted]', cls: 'r' },
      ], pause: 80 },
    { text: '│', cls: 'd', pause: 20 },
    { text: '└──────────────────────────────────────────────────────', cls: 'd', pause: 150 },
    { text: '', pause: 600 },
    // --- sem impact ---
    { text: '$ sem impact authenticateUser', cls: 'cmd', pause: 500, typing: true },
    { text: '', pause: 300 },
    { parts: [
        { text: '⊕ function ', cls: 'd' },
        { text: 'authenticateUser', cls: 'w' },
        { text: ' (src/auth/login.ts:26)', cls: 'd' },
      ], pause: 80 },
    { text: '', pause: 40 },
    { parts: [
        { text: ' → depends on: ', cls: 'd' },
        { text: 'db.findUser', cls: 'b' },
        { text: ', ', cls: 'd' },
        { text: 'rateLimiter.check', cls: 'b' },
      ], pause: 80 },
    { parts: [
        { text: ' ← used by: ', cls: 'd' },
        { text: 'loginRoute', cls: 'b' },
        { text: ', ', cls: 'd' },
        { text: 'authMiddleware', cls: 'b' },
      ], pause: 80 },
    { parts: [
        { text: ' ', cls: '' },
        { text: '! 42 entities transitively affected', cls: 'r' },
      ], pause: 80 },
    { parts: [
        { text: ' ', cls: '' },
        { text: '⚡ 7 tests affected', cls: 'y' },
      ], pause: 150 },
    { text: '', pause: 600 },
    // --- sem blame ---
    { text: '$ sem blame src/auth/login.ts', cls: 'cmd', pause: 500, typing: true },
    { text: '', pause: 300 },
    { text: '┌─ src/auth/login.ts', cls: 'd', pause: 50 },
    { text: '│', cls: 'd', pause: 20 },
    { parts: [
        { text: '│ ', cls: 'd' },
        { text: '⊕', cls: 'g' },
        { text: ' ', cls: '' },
        { text: 'validateToken', cls: 'w' },
        { text: ' ', cls: '' },
        { text: 'a3f91bc', cls: 'b' },
        { text: ' Alice 03-28', cls: 'd' },
      ], pause: 80 },
    { parts: [
        { text: '│ ', cls: 'd' },
        { text: '⊕', cls: 'g' },
        { text: ' ', cls: '' },
        { text: 'authenticateUser', cls: 'w' },
        { text: ' ', cls: '' },
        { text: 'f7d42e0', cls: 'b' },
        { text: ' Bob 02-14', cls: 'd' },
      ], pause: 80 },
    { parts: [
        { text: '│ ', cls: 'd' },
        { text: '⊕', cls: 'g' },
        { text: ' ', cls: '' },
        { text: 'AuthConfig', cls: 'w' },
        { text: ' ', cls: '' },
        { text: 'e1a08f3', cls: 'b' },
        { text: ' Alice 01-09', cls: 'd' },
      ], pause: 80 },
    { text: '│', cls: 'd', pause: 20 },
    { text: '└──────────────────────────────────────────────────────', cls: 'd', pause: 0 },
  ];
  function makeSpan(text, cls) {
    if (!cls) return document.createTextNode(text);
    const s = document.createElement('span');
    s.className = cls;
    s.textContent = text;
    return s;
  }
  function sleep(ms) {
    return new Promise(r => setTimeout(r, ms));
  }
  async function typeText(parent, text, cls) {
    const node = cls ? document.createElement('span') : null;
    if (node) {
      node.className = cls;
      parent.appendChild(node);
    }
    const target = node || parent;
    for (let i = 0; i < text.length; i++) {
      target.textContent += text[i];
      await sleep(30 + Math.random() * 30);
    }
  }
  async function run() {
    for (const line of lines) {
      if (line.typing) {
        await typeText(el, line.text, line.cls);
        el.appendChild(document.createTextNode('\n'));
      } else if (line.parts) {
        for (const part of line.parts) {
          el.appendChild(makeSpan(part.text, part.cls));
        }
        el.appendChild(document.createTextNode('\n'));
      } else {
        el.appendChild(makeSpan(line.text, line.cls));
        el.appendChild(document.createTextNode('\n'));
      }
      if (line.pause) await sleep(line.pause);
    }
    const cursor = document.createElement('span');
    cursor.textContent = '█';
    cursor.style.animation = 'blink 1s step-end infinite';
    el.appendChild(document.createTextNode('$ '));
    el.appendChild(cursor);
  }
  const observer = new IntersectionObserver((entries) => {
    if (entries[0].isIntersecting) {
      observer.disconnect();
      run();
    }
  });
  observer.observe(el);
})();
// Scroll-triggered fade-in (function() {
  const els = docume
```

--------------------------------

### Filter semantic diff by file extensions

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Performs a semantic diff, but only considers files with the specified extensions.

```bash
sem diff --file-exts .py .rs
```

--------------------------------

### JSON output for sem impact

Source: https://github.com/ataraxy-labs/sem/blob/main/README.md

Outputs the results of the `sem impact` command in JSON format.

```bash
sem impact authenticateUser --json
```

--------------------------------

### Agent Accuracy Comparison

Source: https://github.com/ataraxy-labs/sem/blob/main/docs/benchmarks.html

Compares the accuracy of an agent using `sem diff` JSON versus raw `git diff` for various code change analysis questions.

```text
sem diff

git diff

Q1: List added functions (F1) 93% vs 75%

Q2: Files with modified entities (F1) 100% vs 55%

Q3: Entity type counts (accuracy) 91% vs 13%

Q4: Added/modified/deleted counts (exact) 100% vs 22%

Overall average 96% vs 41%
```