diff --git a/README.md b/README.md
index 05e1842..230bc31 100644
--- a/README.md
+++ b/README.md
@@ -47,29 +47,29 @@ The database is automatically created at `.code_search/surrealdb.rocksdb` in you
 Import a call graph JSON file (generated by [ex_ast](https://github.com/CamonZ/ex_ast)):
 
 ```bash
-code_search import --file call_graph.json
+code_search code import --file call_graph.json
 ```
 
 ### 3. Query the data
 
 ```bash
 # Find where a function is defined
-code_search location get_user MyApp.Accounts
+code_search code location get_user MyApp.Accounts
 
 # What does this function call?
-code_search calls-from MyApp.Accounts get_user
+code_search code calls-from MyApp.Accounts get_user
 
 # Who calls this function?
-code_search calls-to MyApp.Repo get
+code_search code calls-to MyApp.Repo get
 
 # Trace the full call chain from a function
-code_search trace MyApp.Web.UserController show
+code_search code trace MyApp.Web.UserController show
 
 # Find unused functions
-code_search unused -P
+code_search code unused -P
 
 # Find hotspots (most called functions)
-code_search hotspots -l 10
+code_search code hotspots -l 10
 ```
 
 ## Output Formats
@@ -82,7 +82,7 @@ All commands support three output formats via `--format` or `-o`:
 
 ## Commands
 
-Use `code_search <command> --help` for detailed help on any command.
+Use `code_search code <command> --help` for detailed help on any command.
 
 ### Query Commands
 
@@ -169,26 +169,26 @@ If `--db` is not specified, commands automatically search for the database in th
 
 ```bash
 # Find all functions that accept a User.t type
-code_search accepts "User.t"
+code_search code accepts "User.t"
 
 # Find modules with circular dependencies
-code_search cycles MyApp.Core
+code_search code cycles MyApp.Core
 
 # Find the most complex functions in a namespace
-code_search complexity MyApp.Accounts --min 10
+code_search code complexity MyApp.Accounts --min 10
 
 # Trace how a controller action flows through the codebase
-code_search trace MyApp.Web.UserController create --depth 10
+code_search code trace MyApp.Web.UserController create --depth 10
 
 # Find all paths from an API endpoint to a database call
-code_search path --from-module MyApp.API --from-function create_user \
+code_search code path --from-module MyApp.API --from-function create_user \
                  --to-module MyApp.Repo --to-function insert
 
 # Find god modules (too large, too connected)
-code_search god-modules --min-functions 30 --min-loc 500
+code_search code god-modules --min-functions 30 --min-loc 500
 
 # Find boundary modules that many depend on
-code_search boundaries --min-ratio 3.0
+code_search code boundaries --min-ratio 3.0
 ```
 
 ## Claude Code Integration
@@ -234,6 +234,22 @@ git config code-search.mix-env test  # Default: dev
 
 See [docs/GIT_HOOKS.md](docs/GIT_HOOKS.md) for detailed documentation and troubleshooting.
 
+### Git Worktrees
+
+When using [git worktrees](https://git-scm.com/docs/git-worktree), each
+worktree must have its own local database. Run setup and import once in
+each worktree directory:
+
+```sh
+mix compile
+ex_ast --output /tmp/call_graph.json
+code_search setup
+code_search code import --file /tmp/call_graph.json
+```
+
+See [docs/WORKTREES.md](docs/WORKTREES.md) for full details and
+troubleshooting.
+
 ### Using with Claude Code
 
 Once templates are installed, Claude Code can automatically help you explore your codebase:
diff --git a/docs/GIT_HOOKS.md b/docs/GIT_HOOKS.md
index 3a3924a..b204b99 100644
--- a/docs/GIT_HOOKS.md
+++ b/docs/GIT_HOOKS.md
@@ -81,7 +81,7 @@ When you make a commit, the post-commit hook:
    - Uses the configured Mix environment
    - Outputs JSON to a temporary file
 
-4. **Updates database**: Runs `code_search import` to update the database
+4. **Updates database**: Runs `code_search code import` to update the database
    - Database path auto-resolves to `.code_search/surrealdb.rocksdb`
    - Uses configured project name if set (optional)
    - Performs upsert operations (updates existing records, inserts new ones)
@@ -224,7 +224,7 @@ mix compile --debug-info
 ex_ast --git-diff HEAD~1 --format json --output changes.json
 
 # Import
-code_search --db call_graph.db import --file changes.json
+code_search --db call_graph.db code import --file changes.json
 ```
 
 Or for a different git reference:
@@ -246,7 +246,7 @@ The same approach works in CI/CD pipelines. Example GitHub Actions workflow:
   run: |
     mix compile --debug-info
     ex_ast --git-diff HEAD~1 --format json --output changes.json
-    code_search --db call_graph.db import --file changes.json
+    code_search --db call_graph.db code import --file changes.json
 ```
 
 ## Performance Characteristics
diff --git a/docs/NEW_COMMANDS.md b/docs/NEW_COMMANDS.md
index 0585982..57104cc 100644
--- a/docs/NEW_COMMANDS.md
+++ b/docs/NEW_COMMANDS.md
@@ -56,7 +56,7 @@ use crate::output::{OutputFormat, Outputable};
 #[derive(Args, Debug)]
 #[command(after_help = "\
 Examples:
-  code_search <name> --arg value    # Example usage")]
+  code_search code <name> --arg value    # Example usage")]
 pub struct <Name>Cmd {
     /// Description of the argument
     #[arg(short, long)]
@@ -148,9 +148,9 @@ impl Outputable for <Name>Result {
 
 See [examples/output_tests.rs.example](./examples/output_tests.rs.example) for a reference showing the snapshot testing pattern. The example includes a helper for generating the actual output values to use in your snapshots.
 
-### 8. Register the command (`src/commands/mod.rs`)
+### 8. Register the command
 
-Add the module declaration and public export:
+Add the module declaration and public export in `src/commands/mod.rs`:
 
 ```rust
 mod <name>;
@@ -158,24 +158,21 @@ mod <name>;
 pub use <name>::<Name>Cmd;
 ```
 
-Add the variant to the `Command` enum:
+Add the variant to the `CodeCommand` enum in `src/commands/code.rs`:
 
 ```rust
 #[derive(Subcommand, Debug)]
 #[enum_dispatch(CommandRunner)]
-pub enum Command {
+pub enum CodeCommand {
     /// Existing commands...
     Import(ImportCmd),
 
     /// Description of your command
     <Name>(<Name>Cmd),
-
-    #[command(external_subcommand)]
-    Unknown(Vec<String>),
 }
 ```
 
-**Note:** The `#[enum_dispatch(CommandRunner)]` attribute is already on the `Command` enum. The `enum_dispatch` crate automatically generates the dispatch logic for all variants. You do NOT need to add a match arm in `Command::run()` - the `CommandRunner` implementation you added to your command's `mod.rs` file (in step 2) is all that's needed!
+**Note:** The top-level `Command` enum in `mod.rs` has only `Setup` and `Code(CodeCommand)`. All code analysis commands are registered in `CodeCommand` (in `code.rs`), not in `Command`. The `#[enum_dispatch(CommandRunner)]` attribute automatically generates dispatch logic for all variants. You do NOT need to add a match arm — the `CommandRunner` implementation you added to your command's `mod.rs` file (in step 2) is all that's needed!
 
 The dispatch is handled entirely by the `enum_dispatch` procedural macro at compile time, which is faster and more maintainable than manual match arms.
 
@@ -184,7 +181,7 @@ The dispatch is handled entirely by the `enum_dispatch` procedural macro at comp
 ```bash
 cargo build
 cargo test
-cargo run -- <name> --help
+cargo run -- code <name> --help
 ```
 
 ## Checklist
@@ -219,7 +216,7 @@ cargo run -- <name> --help
 - [ ] Registered command in `src/commands/mod.rs`
   - [ ] Added module declaration: `mod <name>;`
   - [ ] Added public export: `pub use <name>::<Name>Cmd;`
-  - [ ] Added enum variant to `Command` enum (dispatch is automatic via `#[enum_dispatch(CommandRunner)]`)
+- [ ] Added enum variant to `CodeCommand` in `src/commands/code.rs` (dispatch is automatic via `#[enum_dispatch(CommandRunner)]`)
   - [ ] **No match arm needed** - enum_dispatch handles it automatically!
 - [ ] Verified with `cargo build && cargo test`
 
diff --git a/docs/WORKTREES.md b/docs/WORKTREES.md
new file mode 100644
index 0000000..82132c2
--- /dev/null
+++ b/docs/WORKTREES.md
@@ -0,0 +1,51 @@
+# Using code_search with Git Worktrees
+
+Each worktree must have its own local database. The tool uses an embedded
+RocksDB which only allows one process to hold the lock at a time — if multiple
+worktrees share the global `~/.code_search/surrealdb.rocksdb` you will get:
+
+```
+Error: "Failed to connect to SurrealDB: IO error: While lock file: LOCK:
+Resource temporarily unavailable"
+```
+
+## Setup per worktree
+
+Run this once in each worktree root:
+
+```sh
+mix compile
+ex_ast --output /tmp/call_graph.json
+code_search setup
+code_search code import --file /tmp/call_graph.json
+rm /tmp/call_graph.json
+```
+
+`code_search setup` creates `.code_search/surrealdb.rocksdb` in the current
+directory. The tool's path resolution always prefers a local `.code_search/`
+over the global `~/.code_search/`, so each worktree gets its own isolated
+database and lock file.
+
+## Rebuilding a stale or corrupt database
+
+If you see a "record already exists" or lock error on a worktree that already
+has a local DB:
+
+```sh
+rm -rf .code_search/surrealdb.rocksdb
+mix compile
+ex_ast --output /tmp/call_graph.json
+code_search setup
+code_search code import --file /tmp/call_graph.json
+rm /tmp/call_graph.json
+```
+
+## Important notes
+
+- Never rely on `~/.code_search/surrealdb.rocksdb` in a multi-worktree setup
+- Two processes cannot share the same RocksDB — this is an embedded database
+  limitation, not a bug in code_search
+- Each worktree's `.code_search/` should be in `.gitignore` (it is by default)
+- The git hook installed via `code_search setup --install-hooks` handles
+  incremental updates automatically after each commit, so you only need to do
+  the full import once per worktree
diff --git a/templates/agents/code-search-explorer.md b/templates/agents/code-search-explorer.md
index 2a44679..7df372b 100644
--- a/templates/agents/code-search-explorer.md
+++ b/templates/agents/code-search-explorer.md
@@ -20,11 +20,11 @@ You are an expert Elixir/Erlang codebase explorer powered by the `code_search` C
 When asked to explore a codebase:
 
 1. **Identify the query type**:
-   - Finding definitions → Use `code_search location` or `code_search function`
-   - Understanding calls → Use `code_search calls-from` or `code_search calls-to`
-   - Tracing paths → Use `code_search trace` or `code_search reverse-trace`
-   - Module analysis → Use `code_search browse-module` or `code_search depends-on`
-   - Quality checks → Use `code_search unused`, `code_search hotspots`, etc.
+   - Finding definitions → Use `code_search code location` or `code_search code function`
+   - Understanding calls → Use `code_search code calls-from` or `code_search code calls-to`
+   - Tracing paths → Use `code_search code trace` or `code_search code reverse-trace`
+   - Module analysis → Use `code_search code browse-module` or `code_search code depends-on`
+   - Quality checks → Use `code_search code unused`, `code_search code hotspots`, etc.
 
 2. **Execute queries efficiently**:
    - Always use `--format toon` for token-efficient output
@@ -52,7 +52,7 @@ The database is automatically searched in:
 
 Override if needed:
 ```bash
-code_search --db /path/to/db.rocksdb <command>
+code_search --db /path/to/db.rocksdb code <command>
 ```
 
 ## Example Workflow
@@ -61,17 +61,17 @@ When user asks: "Where is the authenticate function defined and what calls it?"
 
 1. Find definition:
 ```bash
-code_search --format toon location authenticate
+code_search --format toon code location authenticate
 ```
 
 2. Find callers:
 ```bash
-code_search --format toon calls-to --function authenticate
+code_search --format toon code calls-to --function authenticate
 ```
 
 3. If results show a specific module, explore it:
 ```bash
-code_search --format toon browse-module AuthModule
+code_search --format toon code browse-module AuthModule
 ```
 
 4. Read source for context:
@@ -83,17 +83,17 @@ code_search --format toon browse-module AuthModule
 
 | Task | Command |
 |------|---------|
-| Find function | `code_search --format toon location <name>` |
-| Browse module | `code_search --format toon browse-module <module>` |
-| What calls X? | `code_search --format toon calls-to --function <name>` |
-| What does X call? | `code_search --format toon calls-from <module> <function>` |
-| Trace execution | `code_search --format toon trace <module> <function> --depth N` |
-| Find path A→B | `code_search --format toon path --from-module A --to-module B` |
-| Module deps | `code_search --format toon depends-on <module>` |
-| Who depends on X? | `code_search --format toon depended-by <module>` |
-| Unused code | `code_search --format toon unused` |
-| Hotspots | `code_search --format toon hotspots --kind incoming` |
-| Code smells | `code_search --format toon god-modules`, `complexity`, etc. |
+| Find function | `code_search --format toon code location <name>` |
+| Browse module | `code_search --format toon code browse-module <module>` |
+| What calls X? | `code_search --format toon code calls-to --function <name>` |
+| What does X call? | `code_search --format toon code calls-from <module> <function>` |
+| Trace execution | `code_search --format toon code trace <module> <function> --depth N` |
+| Find path A→B | `code_search --format toon code path --from-module A --to-module B` |
+| Module deps | `code_search --format toon code depends-on <module>` |
+| Who depends on X? | `code_search --format toon code depended-by <module>` |
+| Unused code | `code_search --format toon code unused` |
+| Hotspots | `code_search --format toon code hotspots --kind incoming` |
+| Code smells | `code_search --format toon code god-modules`, `complexity`, etc. |
 
 ## Important Notes
 
diff --git a/templates/hooks/post-commit b/templates/hooks/post-commit
index c9d471a..17abbc9 100644
--- a/templates/hooks/post-commit
+++ b/templates/hooks/post-commit
@@ -6,7 +6,7 @@
 # from the last commit. It:
 # 1. Ensures the project is compiled with debug info
 # 2. Extracts AST data for changed files using ex_ast --git-diff
-# 3. Imports the data into the database using code_search import
+# 3. Imports the data into the database using code_search code import
 #
 # Installation:
 #   cp hooks/post-commit .git/hooks/post-commit
@@ -105,7 +105,7 @@ fi
 # Database path will be auto-resolved to .code_search/surrealdb.rocksdb
 info "Importing data..."
 
-if code_search import --file "${TEMP_JSON}" 2>&1; then
+if code_search code import --file "${TEMP_JSON}" 2>&1; then
     info "Database updated successfully!"
 else
     error "Database import failed"
diff --git a/templates/skills/accepts/SKILL.md b/templates/skills/accepts/SKILL.md
index 2eef4ca..7a16a08 100644
--- a/templates/skills/accepts/SKILL.md
+++ b/templates/skills/accepts/SKILL.md
@@ -14,7 +14,7 @@ Find functions that take certain types as input parameters. Use this to understa
 ## Usage
 
 ```bash
-code_search --format toon accepts <PATTERN> [MODULE] [OPTIONS]
+code_search --format toon code accepts <PATTERN> [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -34,10 +34,10 @@ code_search --format toon accepts <PATTERN> [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search accepts "User.t"              # Find functions accepting User.t
-code_search accepts "map()"               # Find functions accepting maps
-code_search accepts "User.t" MyApp        # Filter to module MyApp
-code_search accepts -r "list\(.*\)"       # Regex pattern matching
+code_search code accepts "User.t"              # Find functions accepting User.t
+code_search code accepts "map()"               # Find functions accepting maps
+code_search code accepts "User.t" MyApp        # Filter to module MyApp
+code_search code accepts -r "list\(.*\)"       # Regex pattern matching
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/boundaries/SKILL.md b/templates/skills/boundaries/SKILL.md
index d241643..900e9e3 100644
--- a/templates/skills/boundaries/SKILL.md
+++ b/templates/skills/boundaries/SKILL.md
@@ -14,7 +14,7 @@ Identify modules that act as architectural boundaries - modules that are heavily
 ## Usage
 
 ```bash
-code_search --format toon boundaries [MODULE] [OPTIONS]
+code_search --format toon code boundaries [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -35,11 +35,11 @@ code_search --format toon boundaries [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search boundaries                          # Find all boundary modules
-code_search boundaries MyApp.Web                # Filter to MyApp.Web namespace
-code_search boundaries --min-incoming 5         # With minimum 5 incoming calls
-code_search boundaries --min-ratio 2.0          # With minimum 2.0 ratio
-code_search boundaries -l 20                    # Show top 20 boundary modules
+code_search code boundaries                          # Find all boundary modules
+code_search code boundaries MyApp.Web                # Filter to MyApp.Web namespace
+code_search code boundaries --min-incoming 5         # With minimum 5 incoming calls
+code_search code boundaries --min-ratio 2.0          # With minimum 2.0 ratio
+code_search code boundaries -l 20                    # Show top 20 boundary modules
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/browse-module/SKILL.md b/templates/skills/browse-module/SKILL.md
index 94f3297..0a7ba9c 100644
--- a/templates/skills/browse-module/SKILL.md
+++ b/templates/skills/browse-module/SKILL.md
@@ -14,7 +14,7 @@ Get a complete overview of all functions, specs, types, and structs in a specifi
 ## Usage
 
 ```bash
-code_search --format toon browse-module <MODULE_OR_FILE> [OPTIONS]
+code_search --format toon code browse-module <MODULE_OR_FILE> [OPTIONS]
 ```
 
 ## Arguments
diff --git a/templates/skills/calls-from/skill.md b/templates/skills/calls-from/skill.md
index 84aa705..83c5c66 100644
--- a/templates/skills/calls-from/skill.md
+++ b/templates/skills/calls-from/skill.md
@@ -8,7 +8,7 @@ description: Show what a module/function calls (outgoing edges). Use to understa
 ## All Calls from a Module
 
 ```bash
-code_search --format toon calls-from Phoenix.Endpoint.RenderErrors
+code_search --format toon code calls-from Phoenix.Endpoint.RenderErrors
 ```
 
 Output:
@@ -24,13 +24,13 @@ calls[22]{call_type,callee_arity,callee_function,callee_module,caller_function,c
 ## Calls from a Specific Function
 
 ```bash
-code_search --format toon calls-from Phoenix.Controller render
+code_search --format toon code calls-from Phoenix.Controller render
 ```
 
 ## With Specific Arity
 
 ```bash
-code_search --format toon calls-from Phoenix.Controller render 3
+code_search --format toon code calls-from Phoenix.Controller render 3
 ```
 
 ## Understanding Call Types
@@ -41,7 +41,7 @@ code_search --format toon calls-from Phoenix.Controller render 3
 ## Tracing Error Handling Flow
 
 ```bash
-code_search --format toon calls-from Phoenix.Endpoint.RenderErrors "__catch__"
+code_search --format toon code calls-from Phoenix.Endpoint.RenderErrors "__catch__"
 ```
 
 This shows what happens when an error is caught - the error handling chain.
diff --git a/templates/skills/calls-to/skill.md b/templates/skills/calls-to/skill.md
index 3af24e8..a36d65f 100644
--- a/templates/skills/calls-to/skill.md
+++ b/templates/skills/calls-to/skill.md
@@ -8,7 +8,7 @@ description: Show what calls a module/function (incoming edges). Use to find cal
 ## Find All Callers of a Function
 
 ```bash
-code_search --format toon calls-to Mix.Phoenix copy_from
+code_search --format toon code calls-to Mix.Phoenix copy_from
 ```
 
 Output:
@@ -23,19 +23,19 @@ calls[14]{call_type,callee_arity,callee_function,callee_module,caller_function,c
 ## Find All Callers of a Module
 
 ```bash
-code_search --format toon calls-to Phoenix.Controller
+code_search --format toon code calls-to Phoenix.Controller
 ```
 
 ## Find Callers with Specific Arity
 
 ```bash
-code_search --format toon calls-to Phoenix.Controller render 3
+code_search --format toon code calls-to Phoenix.Controller render 3
 ```
 
 ## Find Internal Recursive Calls
 
 ```bash
-code_search --format toon calls-to Phoenix.Channel reply
+code_search --format toon code calls-to Phoenix.Channel reply
 ```
 
 Output shows `Phoenix.Channel.reply/2` calling itself (clause delegation):
diff --git a/templates/skills/clusters/SKILL.md b/templates/skills/clusters/SKILL.md
index 7da595a..2c14bb3 100644
--- a/templates/skills/clusters/SKILL.md
+++ b/templates/skills/clusters/SKILL.md
@@ -14,7 +14,7 @@ Group modules by their namespace/prefix to understand how different parts of the
 ## Usage
 
 ```bash
-code_search --format toon clusters [MODULE] [OPTIONS]
+code_search --format toon code clusters [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -35,11 +35,11 @@ code_search --format toon clusters [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search clusters                      # Show all namespace clusters
-code_search clusters MyApp.Core           # Filter to MyApp.Core namespace
-code_search clusters --depth 2            # Cluster at depth 2 (e.g., MyApp.Accounts)
-code_search clusters --depth 3            # Cluster at depth 3 (e.g., MyApp.Accounts.Auth)
-code_search clusters --show-dependencies  # Include cross-namespace call counts
+code_search code clusters                      # Show all namespace clusters
+code_search code clusters MyApp.Core           # Filter to MyApp.Core namespace
+code_search code clusters --depth 2            # Cluster at depth 2 (e.g., MyApp.Accounts)
+code_search code clusters --depth 3            # Cluster at depth 3 (e.g., MyApp.Accounts.Auth)
+code_search code clusters --show-dependencies  # Include cross-namespace call counts
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/code-search-explorer/SKILL.md b/templates/skills/code-search-explorer/SKILL.md
index 87f7cf4..abf1106 100644
--- a/templates/skills/code-search-explorer/SKILL.md
+++ b/templates/skills/code-search-explorer/SKILL.md
@@ -35,12 +35,12 @@ The codebase must have a call graph extracted and imported:
 2. **Import into database**:
    ```bash
    code_search setup
-   code_search import --file call_graph.json
+   code_search code import --file call_graph.json
    ```
 
 3. **Verify setup**:
    ```bash
-   code_search search ""  # Should return modules if data is imported
+   code_search code search ""  # Should return modules if data is imported
    ```
 
 ## Quick Examples
@@ -51,7 +51,7 @@ The codebase must have a call graph extracted and imported:
 Where is the process_payment function defined?
 ```
 
-**What happens**: Agent runs `code_search --format toon location process_payment` and shows you the file path and line number.
+**What happens**: Agent runs `code_search --format toon code location process_payment` and shows you the file path and line number.
 
 ### Understanding Call Relationships
 
@@ -59,7 +59,7 @@ Where is the process_payment function defined?
 What functions call create_user?
 ```
 
-**What happens**: Agent runs `code_search --format toon calls-to --function create_user` and lists all callers with locations.
+**What happens**: Agent runs `code_search --format toon code calls-to --function create_user` and lists all callers with locations.
 
 ### Tracing Execution Flow
 
@@ -67,7 +67,7 @@ What functions call create_user?
 Trace the execution path from handle_request in ApiController
 ```
 
-**What happens**: Agent runs `code_search --format toon trace ApiController handle_request --depth 3` showing the full call tree.
+**What happens**: Agent runs `code_search --format toon code trace ApiController handle_request --depth 3` showing the full call tree.
 
 ### Module Analysis
 
@@ -75,7 +75,7 @@ Trace the execution path from handle_request in ApiController
 Show me everything in the Authentication module
 ```
 
-**What happens**: Agent runs `code_search --format toon browse-module Authentication` listing all public functions, types, and specs.
+**What happens**: Agent runs `code_search --format toon code browse-module Authentication` listing all public functions, types, and specs.
 
 ### Dependency Analysis
 
@@ -83,7 +83,7 @@ Show me everything in the Authentication module
 What modules does PaymentGateway depend on?
 ```
 
-**What happens**: Agent runs `code_search --format toon depends-on PaymentGateway` showing direct and transitive dependencies.
+**What happens**: Agent runs `code_search --format toon code depends-on PaymentGateway` showing direct and transitive dependencies.
 
 ### Finding Dead Code
 
@@ -91,7 +91,7 @@ What modules does PaymentGateway depend on?
 Find unused functions in this codebase
 ```
 
-**What happens**: Agent runs `code_search --format toon unused` listing functions with zero callers.
+**What happens**: Agent runs `code_search --format toon code unused` listing functions with zero callers.
 
 ### Code Quality Checks
 
@@ -167,17 +167,17 @@ The agent uses `--format toon` for token efficiency, but you can also run comman
 
 - **Table** (default): Human-readable output
   ```bash
-  code_search location authenticate
+  code_search code location authenticate
   ```
 
 - **JSON**: For scripts/tools
   ```bash
-  code_search --format json location authenticate
+  code_search --format json code location authenticate
   ```
 
 - **Toon**: Token-efficient for LLMs (what the agent uses)
   ```bash
-  code_search --format toon location authenticate
+  code_search --format toon code location authenticate
   ```
 
 ## Database Configuration
@@ -189,7 +189,7 @@ Database is automatically searched in this order:
 
 Override with `--db` flag if needed:
 ```bash
-code_search --db /path/to/db.rocksdb <command>
+code_search --db /path/to/db.rocksdb code <command>
 ```
 
 ## Tips for Best Results
@@ -215,17 +215,17 @@ You can also run `code_search` directly:
 ```bash
 # Get help
 code_search --help
-code_search <command> --help
+code_search code <command> --help
 
 # Common queries
-code_search location my_function
-code_search browse-module MyApp.Module
-code_search calls-to --function process
-code_search trace MyModule process --depth 2
-code_search depends-on MyApp.Core
-code_search unused
-code_search hotspots --kind incoming --limit 20
-code_search god-modules
+code_search code location my_function
+code_search code browse-module MyApp.Module
+code_search code calls-to --function process
+code_search code trace MyModule process --depth 2
+code_search code depends-on MyApp.Core
+code_search code unused
+code_search code hotspots --kind incoming --limit 20
+code_search code god-modules
 ```
 
 ## Related Resources
@@ -242,9 +242,9 @@ code_search god-modules
 **Question**: "How does authentication work in this app?"
 
 **Agent workflow**:
-1. `code_search --format toon search auth` → Find auth-related modules
-2. `code_search --format toon browse-module AuthController` → See public interface
-3. `code_search --format toon trace AuthController login` → Follow login flow
+1. `code_search --format toon code search auth` → Find auth-related modules
+2. `code_search --format toon code browse-module AuthController` → See public interface
+3. `code_search --format toon code trace AuthController login` → Follow login flow
 4. Read relevant source files for implementation details
 5. Summarize the authentication flow
 
@@ -253,8 +253,8 @@ code_search god-modules
 **Question**: "Can I safely delete the User.send_notification function?"
 
 **Agent workflow**:
-1. `code_search --format toon calls-to --function send_notification` → Find callers
-2. `code_search --format toon reverse-trace User send_notification` → Full reverse tree
+1. `code_search --format toon code calls-to --function send_notification` → Find callers
+2. `code_search --format toon code reverse-trace User send_notification` → Full reverse tree
 3. Report: "This function is called from 3 places: OrderController, AlertService, and AdminPanel"
 4. User can decide based on impact
 
@@ -263,8 +263,8 @@ code_search god-modules
 **Question**: "What code can I delete from the Reports module?"
 
 **Agent workflow**:
-1. `code_search --format toon unused --module Reports` → Find unused functions
-2. `code_search --format toon browse-module Reports` → Show all functions
+1. `code_search --format toon code unused --module Reports` → Find unused functions
+2. `code_search --format toon code browse-module Reports` → Show all functions
 3. Compare and identify private functions with zero callers
 4. Report candidates for deletion with file paths
 
@@ -274,7 +274,7 @@ code_search god-modules
 - **Solution**: Run `code_search setup` first (creates `.code_search/surrealdb.rocksdb`)
 
 **Issue**: "No results found"
-- **Solution**: Check if data is imported with `code_search search ""`
+- **Solution**: Check if data is imported with `code_search code search ""`
 - **Solution**: Try broader search terms or remove filters
 
 **Issue**: "Too many results"
diff --git a/templates/skills/code-search-explorer/reference.md b/templates/skills/code-search-explorer/reference.md
index 27fab60..adc907c 100644
--- a/templates/skills/code-search-explorer/reference.md
+++ b/templates/skills/code-search-explorer/reference.md
@@ -4,46 +4,46 @@
 
 ### Discovery & Search
 ```bash
-code_search search <pattern>              # Find modules/functions by name
-code_search browse-module <module>        # Show module contents
-code_search location <function>           # Find where function is defined
-code_search function <module> <function>  # Get function details
+code_search code search <pattern>              # Find modules/functions by name
+code_search code browse-module <module>        # Show module contents
+code_search code location <function>           # Find where function is defined
+code_search code function <module> <function>  # Get function details
 ```
 
 ### Call Graph Navigation
 ```bash
-code_search calls-from <module> <function>          # What does X call?
-code_search calls-to --function <name>              # What calls X?
-code_search trace <module> <function> --depth N     # Forward call tree
-code_search reverse-trace <module> <function>       # Backward call tree
-code_search path --from-module A --to-module B      # Find call path A→B
+code_search code calls-from <module> <function>          # What does X call?
+code_search code calls-to --function <name>              # What calls X?
+code_search code trace <module> <function> --depth N     # Forward call tree
+code_search code reverse-trace <module> <function>       # Backward call tree
+code_search code path --from-module A --to-module B      # Find call path A→B
 ```
 
 ### Module Dependencies
 ```bash
-code_search depends-on <module>           # What does module depend on?
-code_search depended-by <module>          # What depends on module?
-code_search clusters                      # Find module clusters
-code_search cycles                        # Find circular dependencies
-code_search boundaries                    # Identify architectural boundaries
+code_search code depends-on <module>           # What does module depend on?
+code_search code depended-by <module>          # What depends on module?
+code_search code clusters                      # Find module clusters
+code_search code cycles                        # Find circular dependencies
+code_search code boundaries                    # Identify architectural boundaries
 ```
 
 ### Code Quality
 ```bash
-code_search unused                        # Find unused functions
-code_search hotspots --kind <type>        # Find coupling hotspots
-code_search god-modules                   # Find overly large modules
-code_search complexity                    # Find complex functions
-code_search large-functions               # Find long functions
-code_search many-clauses                  # Functions with many clauses
-code_search duplicates                    # Find duplicate signatures
+code_search code unused                        # Find unused functions
+code_search code hotspots --kind <type>        # Find coupling hotspots
+code_search code god-modules                   # Find overly large modules
+code_search code complexity                    # Find complex functions
+code_search code large-functions               # Find long functions
+code_search code many-clauses                  # Functions with many clauses
+code_search code duplicates                    # Find duplicate signatures
 ```
 
 ### Type Analysis
 ```bash
-code_search accepts <type-pattern>        # Functions accepting a type
-code_search returns <type-pattern>        # Functions returning a type
-code_search struct-usage <struct>         # Where is struct used?
+code_search code accepts <type-pattern>        # Functions accepting a type
+code_search code returns <type-pattern>        # Functions returning a type
+code_search code struct-usage <struct>         # Where is struct used?
 ```
 
 ## Global Flags
@@ -74,19 +74,19 @@ code_search struct-usage <struct>         # Where is struct used?
 
 ### Table (Human-readable)
 ```bash
-code_search location authenticate
+code_search code location authenticate
 # Shows: module, function, file, line in a table
 ```
 
 ### JSON (Programmatic)
 ```bash
-code_search --format json location authenticate
+code_search --format json code location authenticate
 # Returns structured JSON
 ```
 
 ### Toon (Token-efficient for LLMs)
 ```bash
-code_search --format toon location authenticate
+code_search --format toon code location authenticate
 # Returns compact format:
 # results[1]:
 #   module: MyApp.Auth
@@ -100,42 +100,42 @@ code_search --format toon location authenticate
 ### Find and Explore a Function
 ```bash
 # 1. Find it
-code_search location authenticate
+code_search code location authenticate
 
 # 2. See what it calls
-code_search calls-from MyApp.Auth authenticate
+code_search code calls-from MyApp.Auth authenticate
 
 # 3. See what calls it
-code_search calls-to --function authenticate
+code_search code calls-to --function authenticate
 
 # 4. Trace its execution
-code_search trace MyApp.Auth authenticate --depth 2
+code_search code trace MyApp.Auth authenticate --depth 2
 ```
 
 ### Module Impact Analysis
 ```bash
 # 1. What does it contain?
-code_search browse-module MyApp.Payment
+code_search code browse-module MyApp.Payment
 
 # 2. What does it depend on?
-code_search depends-on MyApp.Payment
+code_search code depends-on MyApp.Payment
 
 # 3. What depends on it?
-code_search depended-by MyApp.Payment
+code_search code depended-by MyApp.Payment
 
 # 4. Any circular deps?
-code_search cycles
+code_search code cycles
 ```
 
 ### Code Quality Audit
 ```bash
 # Find all quality issues
-code_search unused
-code_search god-modules
-code_search complexity --limit 20
-code_search large-functions --limit 10
-code_search cycles
-code_search hotspots --kind total --limit 15
+code_search code unused
+code_search code god-modules
+code_search code complexity --limit 20
+code_search code large-functions --limit 10
+code_search code cycles
+code_search code hotspots --kind total --limit 15
 ```
 
 ## Tips
@@ -152,12 +152,12 @@ code_search hotspots --kind total --limit 15
 code_search setup
 
 # Import call graph data (from ex_ast)
-code_search import --file call_graph.json
+code_search code import --file call_graph.json
 ```
 
 ## Need More Help?
 
 ```bash
 code_search --help                    # General help
-code_search <command> --help          # Command-specific help
+code_search code <command> --help          # Command-specific help
 ```
diff --git a/templates/skills/complexity/SKILL.md b/templates/skills/complexity/SKILL.md
index 3bc5b62..dc27d3d 100644
--- a/templates/skills/complexity/SKILL.md
+++ b/templates/skills/complexity/SKILL.md
@@ -14,7 +14,7 @@ Analyze function complexity to identify potentially problematic or hard-to-maint
 ## Usage
 
 ```bash
-code_search --format toon complexity [MODULE] [OPTIONS]
+code_search --format toon code complexity [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -36,12 +36,12 @@ code_search --format toon complexity [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search complexity                      # Show all functions with complexity >= 1
-code_search complexity MyApp.Accounts       # Filter to MyApp.Accounts module
-code_search complexity --min 10             # Show functions with complexity >= 10
-code_search complexity --min-depth 3        # Show functions with nesting depth >= 3
-code_search complexity --exclude-generated  # Exclude macro-generated functions
-code_search complexity -l 20                # Show top 20 most complex functions
+code_search code complexity                      # Show all functions with complexity >= 1
+code_search code complexity MyApp.Accounts       # Filter to MyApp.Accounts module
+code_search code complexity --min 10             # Show functions with complexity >= 10
+code_search code complexity --min-depth 3        # Show functions with nesting depth >= 3
+code_search code complexity --exclude-generated  # Exclude macro-generated functions
+code_search code complexity -l 20                # Show top 20 most complex functions
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/cycles/SKILL.md b/templates/skills/cycles/SKILL.md
index fd7fd18..849a6ba 100644
--- a/templates/skills/cycles/SKILL.md
+++ b/templates/skills/cycles/SKILL.md
@@ -14,7 +14,7 @@ Find circular dependencies in the module graph that can cause compilation issues
 ## Usage
 
 ```bash
-code_search --format toon cycles [MODULE] [OPTIONS]
+code_search --format toon code cycles [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -35,10 +35,10 @@ code_search --format toon cycles [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search cycles                            # Find all cycles
-code_search cycles MyApp.Core                 # Filter to MyApp.Core namespace
-code_search cycles --max-length 3             # Only show cycles of length <= 3
-code_search cycles --involving MyApp.Accounts # Only cycles involving Accounts
+code_search code cycles                            # Find all cycles
+code_search code cycles MyApp.Core                 # Filter to MyApp.Core namespace
+code_search code cycles --max-length 3             # Only show cycles of length <= 3
+code_search code cycles --involving MyApp.Accounts # Only cycles involving Accounts
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/depended-by/skill.md b/templates/skills/depended-by/skill.md
index 5e903a0..17a23dd 100644
--- a/templates/skills/depended-by/skill.md
+++ b/templates/skills/depended-by/skill.md
@@ -3,7 +3,7 @@
 ## Find Dependents of a Module
 
 ```bash
-code_search --format toon depended-by Phoenix.Controller
+code_search --format toon code depended-by Phoenix.Controller
 ```
 
 Output:
@@ -17,7 +17,7 @@ dependents[3]{call_count,module,project}:
 ## Find Dependents with Regex
 
 ```bash
-code_search --format toon depended-by 'Ecto\..*' --regex
+code_search --format toon code depended-by 'Ecto\..*' --regex
 ```
 
 ## Understanding the Output
@@ -29,7 +29,7 @@ code_search --format toon depended-by 'Ecto\..*' --regex
 
 Before changing `Phoenix.Controller`:
 ```bash
-code_search --format toon depended-by Phoenix.Controller
+code_search --format toon code depended-by Phoenix.Controller
 ```
 
 Shows 3 modules with 17 total calls would be affected.
@@ -38,7 +38,7 @@ Shows 3 modules with 17 total calls would be affected.
 
 Modules with many dependents are core infrastructure:
 ```bash
-code_search --format toon depended-by MyApp.Repo
+code_search --format toon code depended-by MyApp.Repo
 ```
 
 If many modules depend on Repo, it's a central piece of the architecture.
diff --git a/templates/skills/depends-on/skill.md b/templates/skills/depends-on/skill.md
index 948f71e..736813e 100644
--- a/templates/skills/depends-on/skill.md
+++ b/templates/skills/depends-on/skill.md
@@ -3,7 +3,7 @@
 ## Find Module Dependencies
 
 ```bash
-code_search --format toon depends-on Phoenix.Channel
+code_search --format toon code depends-on Phoenix.Channel
 ```
 
 Output:
@@ -15,7 +15,7 @@ dependencies[1]{call_count,module,project}:
 ## Find Dependencies of Multiple Modules
 
 ```bash
-code_search --format toon depends-on 'Phoenix\.Controller.*' --regex
+code_search --format toon code depends-on 'Phoenix\.Controller.*' --regex
 ```
 
 ## Understanding the Output
@@ -29,7 +29,7 @@ Higher call counts indicate stronger coupling.
 
 Check what a core module depends on:
 ```bash
-code_search --format toon depends-on MyApp.Accounts
+code_search --format toon code depends-on MyApp.Accounts
 ```
 
 This reveals:
diff --git a/templates/skills/duplicates/SKILL.md b/templates/skills/duplicates/SKILL.md
index ae2d9f6..ff812e0 100644
--- a/templates/skills/duplicates/SKILL.md
+++ b/templates/skills/duplicates/SKILL.md
@@ -14,7 +14,7 @@ Identify code duplication to find opportunities for refactoring and consolidatio
 ## Usage
 
 ```bash
-code_search --format toon duplicates [MODULE] [OPTIONS]
+code_search --format toon code duplicates [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -36,11 +36,11 @@ code_search --format toon duplicates [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search duplicates                       # Find all duplicate functions
-code_search duplicates MyApp                 # Filter to specific module
-code_search duplicates --by-module           # Rank modules by duplication
-code_search duplicates --exact               # Use exact source matching
-code_search duplicates --exclude-generated   # Exclude macro-generated functions
+code_search code duplicates                       # Find all duplicate functions
+code_search code duplicates MyApp                 # Filter to specific module
+code_search code duplicates --by-module           # Rank modules by duplication
+code_search code duplicates --exact               # Use exact source matching
+code_search code duplicates --exclude-generated   # Exclude macro-generated functions
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/function/skill.md b/templates/skills/function/skill.md
index 0fe31c8..873f444 100644
--- a/templates/skills/function/skill.md
+++ b/templates/skills/function/skill.md
@@ -3,7 +3,7 @@
 ## Get Function Signature
 
 ```bash
-code_search --format toon function Phoenix.Controller render
+code_search --format toon code function Phoenix.Controller render
 ```
 
 Output:
@@ -16,7 +16,7 @@ functions[2]{args,arity,module,name,project,return_type}:
 ## Filter by Arity
 
 ```bash
-code_search --format toon function Phoenix.Controller render --arity 2
+code_search --format toon code function Phoenix.Controller render --arity 2
 ```
 
 Output:
@@ -28,7 +28,7 @@ functions[1]{args,arity,module,name,project,return_type}:
 ## Regex Search for Multiple Functions
 
 ```bash
-code_search --format toon function Phoenix.Controller 'put_.*' --regex
+code_search --format toon code function Phoenix.Controller 'put_.*' --regex
 ```
 
 ## Understanding the Output
diff --git a/templates/skills/god-modules/SKILL.md b/templates/skills/god-modules/SKILL.md
index 294ee3a..7b8990b 100644
--- a/templates/skills/god-modules/SKILL.md
+++ b/templates/skills/god-modules/SKILL.md
@@ -14,7 +14,7 @@ Identify modules that violate single responsibility principle by having too many
 ## Usage
 
 ```bash
-code_search --format toon god-modules [MODULE] [OPTIONS]
+code_search --format toon code god-modules [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -36,12 +36,12 @@ code_search --format toon god-modules [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search god-modules                         # Find all god modules
-code_search god-modules MyApp.Core              # Filter to MyApp.Core namespace
-code_search god-modules --min-functions 30      # With minimum 30 functions
-code_search god-modules --min-loc 500           # With minimum 500 lines of code
-code_search god-modules --min-total 15          # With minimum 15 total connectivity
-code_search god-modules -l 20                   # Show top 20 god modules
+code_search code god-modules                         # Find all god modules
+code_search code god-modules MyApp.Core              # Filter to MyApp.Core namespace
+code_search code god-modules --min-functions 30      # With minimum 30 functions
+code_search code god-modules --min-loc 500           # With minimum 500 lines of code
+code_search code god-modules --min-total 15          # With minimum 15 total connectivity
+code_search code god-modules -l 20                   # Show top 20 god modules
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/hotspots/skill.md b/templates/skills/hotspots/skill.md
index 8e5d5ce..396f625 100644
--- a/templates/skills/hotspots/skill.md
+++ b/templates/skills/hotspots/skill.md
@@ -3,7 +3,7 @@
 ## Find Most Called Functions
 
 ```bash
-code_search --format toon hotspots
+code_search --format toon code hotspots
 ```
 
 Output:
@@ -20,7 +20,7 @@ hotspots[20]{function,incoming,module,outgoing,total}:
 ## Find Functions with High Fan-Out
 
 ```bash
-code_search --format toon hotspots --kind outgoing
+code_search --format toon code hotspots --kind outgoing
 ```
 
 Functions that call many other functions - potential god functions to refactor.
@@ -28,13 +28,13 @@ Functions that call many other functions - potential god functions to refactor.
 ## Find Total Connections
 
 ```bash
-code_search --format toon hotspots --kind total
+code_search --format toon code hotspots --kind total
 ```
 
 ## Find Boundary Functions
 
 ```bash
-code_search --format toon hotspots --kind ratio
+code_search --format toon code hotspots --kind ratio
 ```
 
 Functions with high incoming/outgoing ratio - these are API boundaries.
@@ -42,7 +42,7 @@ Functions with high incoming/outgoing ratio - these are API boundaries.
 ## Filter to Specific Module Namespace
 
 ```bash
-code_search --format toon hotspots Phoenix.Router
+code_search --format toon code hotspots Phoenix.Router
 ```
 
 ## Understanding the Output
@@ -55,22 +55,22 @@ code_search --format toon hotspots Phoenix.Router
 
 **Find Core Utilities:**
 ```bash
-code_search --format toon hotspots --kind incoming -l 10
+code_search --format toon code hotspots --kind incoming -l 10
 ```
 
 **Find Complex Functions (high fan-out):**
 ```bash
-code_search --format toon hotspots --kind outgoing -l 10
+code_search --format toon code hotspots --kind outgoing -l 10
 ```
 
 **Find Coupling Hotspots:**
 ```bash
-code_search --format toon hotspots --kind total -l 10
+code_search --format toon code hotspots --kind total -l 10
 ```
 
 **Find Boundary Functions:**
 ```bash
-code_search --format toon hotspots --kind ratio -l 10
+code_search --format toon code hotspots --kind ratio -l 10
 ```
 
 ## Options Reference
diff --git a/templates/skills/import/skill.md b/templates/skills/import/skill.md
index 8343679..f52fe2a 100644
--- a/templates/skills/import/skill.md
+++ b/templates/skills/import/skill.md
@@ -3,7 +3,7 @@
 ## Basic Import
 
 ```bash
-code_search --format toon import --file extracted_trace.json
+code_search --format toon code import --file extracted_trace.json
 ```
 
 Output:
@@ -23,13 +23,13 @@ types_imported: 27
 Replace all existing data:
 
 ```bash
-code_search --format toon import --file call_graph.json --clear
+code_search --format toon code import --file call_graph.json --clear
 ```
 
 ## Import to Specific Database
 
 ```bash
-code_search --db /path/to/my.db --format toon import --file call_graph.json
+code_search --db /path/to/my.db --format toon code import --file call_graph.json
 ```
 
 ## Expected JSON Structure
diff --git a/templates/skills/large-functions/SKILL.md b/templates/skills/large-functions/SKILL.md
index e6f6860..afd5711 100644
--- a/templates/skills/large-functions/SKILL.md
+++ b/templates/skills/large-functions/SKILL.md
@@ -14,7 +14,7 @@ Identify functions that are too long or complex based on line count. Use this to
 ## Usage
 
 ```bash
-code_search --format toon large-functions [MODULE] [OPTIONS]
+code_search --format toon code large-functions [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -35,11 +35,11 @@ code_search --format toon large-functions [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search large-functions                     # Find functions with 50+ lines
-code_search large-functions MyApp.Web           # Filter to MyApp.Web namespace
-code_search large-functions --min-lines 100     # Find functions with 100+ lines
-code_search large-functions --include-generated # Include macro-generated functions
-code_search large-functions -l 20               # Show top 20 largest functions
+code_search code large-functions                     # Find functions with 50+ lines
+code_search code large-functions MyApp.Web           # Filter to MyApp.Web namespace
+code_search code large-functions --min-lines 100     # Find functions with 100+ lines
+code_search code large-functions --include-generated # Include macro-generated functions
+code_search code large-functions -l 20               # Show top 20 largest functions
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/location/skill.md b/templates/skills/location/skill.md
index b59f7fc..76d5e45 100644
--- a/templates/skills/location/skill.md
+++ b/templates/skills/location/skill.md
@@ -3,7 +3,7 @@
 ## Find All Definitions of a Function
 
 ```bash
-code_search --format toon location render
+code_search --format toon code location render
 ```
 
 Output:
@@ -18,7 +18,7 @@ locations[15]{arity,end_line,file,guard,kind,module,name,pattern,project,start_l
 ## Find in Specific Module
 
 ```bash
-code_search --format toon location reply Phoenix.Channel
+code_search --format toon code location reply Phoenix.Channel
 ```
 
 Output:
@@ -31,13 +31,13 @@ locations[2]{arity,end_line,file,guard,kind,module,name,pattern,project,start_li
 ## Find with Specific Arity
 
 ```bash
-code_search --format toon location render Phoenix.Controller --arity 3
+code_search --format toon code location render Phoenix.Controller --arity 3
 ```
 
 ## Regex Pattern for Multiple Functions
 
 ```bash
-code_search --format toon location 'handle_.*' --regex --limit 20
+code_search --format toon code location 'handle_.*' --regex --limit 20
 ```
 
 ## Understanding the Output
diff --git a/templates/skills/many-clauses/SKILL.md b/templates/skills/many-clauses/SKILL.md
index aefdfd3..1b9254c 100644
--- a/templates/skills/many-clauses/SKILL.md
+++ b/templates/skills/many-clauses/SKILL.md
@@ -14,7 +14,7 @@ Identify functions with many pattern matching clauses that may be complex or har
 ## Usage
 
 ```bash
-code_search --format toon many-clauses [MODULE] [OPTIONS]
+code_search --format toon code many-clauses [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -35,11 +35,11 @@ code_search --format toon many-clauses [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search many-clauses                     # Find functions with 5+ clauses
-code_search many-clauses MyApp.Web           # Filter to MyApp.Web namespace
-code_search many-clauses --min-clauses 10    # Find functions with 10+ clauses
-code_search many-clauses --include-generated # Include macro-generated functions
-code_search many-clauses -l 20               # Show top 20 functions with most clauses
+code_search code many-clauses                     # Find functions with 5+ clauses
+code_search code many-clauses MyApp.Web           # Filter to MyApp.Web namespace
+code_search code many-clauses --min-clauses 10    # Find functions with 10+ clauses
+code_search code many-clauses --include-generated # Include macro-generated functions
+code_search code many-clauses -l 20               # Show top 20 functions with most clauses
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/path/skill.md b/templates/skills/path/skill.md
index 3d5971b..f2032b1 100644
--- a/templates/skills/path/skill.md
+++ b/templates/skills/path/skill.md
@@ -3,7 +3,7 @@
 ## Find Path Between Two Functions
 
 ```bash
-code_search --format toon path \
+code_search --format toon code path \
   --from-module MyApp.Web.UserController \
   --from-function create \
   --to-module Ecto.Repo \
@@ -25,7 +25,7 @@ to_module: Ecto.Repo
 ## No Path Found
 
 ```bash
-code_search --format toon path \
+code_search --format toon code path \
   --from-module Phoenix.Channel \
   --from-function join \
   --to-module Mix.Tasks.Compile \
@@ -43,7 +43,7 @@ Empty results means no path exists within the search depth.
 ## With Specific Arities
 
 ```bash
-code_search --format toon path \
+code_search --format toon code path \
   --from-module MyApp.API --from-function handle --from-arity 2 \
   --to-module MyApp.Repo --to-function get --to-arity 2 \
   --depth 15
diff --git a/templates/skills/returns/SKILL.md b/templates/skills/returns/SKILL.md
index 3725c4e..989e3ab 100644
--- a/templates/skills/returns/SKILL.md
+++ b/templates/skills/returns/SKILL.md
@@ -14,7 +14,7 @@ Find functions that return values of certain types. Use this to understand what
 ## Usage
 
 ```bash
-code_search --format toon returns <PATTERN> [MODULE] [OPTIONS]
+code_search --format toon code returns <PATTERN> [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -34,10 +34,10 @@ code_search --format toon returns <PATTERN> [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search returns "User.t"              # Find functions returning User.t
-code_search returns "nil"                 # Find functions returning nil
-code_search returns "{:error" MyApp       # Filter to module MyApp
-code_search returns -r "list\(.*\)"       # Regex pattern matching
+code_search code returns "User.t"              # Find functions returning User.t
+code_search code returns "nil"                 # Find functions returning nil
+code_search code returns "{:error" MyApp       # Filter to module MyApp
+code_search code returns -r "list\(.*\)"       # Regex pattern matching
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/reverse-trace/skill.md b/templates/skills/reverse-trace/skill.md
index d3c5eaa..73005f7 100644
--- a/templates/skills/reverse-trace/skill.md
+++ b/templates/skills/reverse-trace/skill.md
@@ -3,7 +3,7 @@
 ## Find All Paths to a Function
 
 ```bash
-code_search --format toon reverse-trace Phoenix.Controller render --depth 3
+code_search --format toon code reverse-trace Phoenix.Controller render --depth 3
 ```
 
 Output:
@@ -22,7 +22,7 @@ calls[18]{callee_arity,callee_function,callee_module,caller_function,caller_kind
 ## Deeper Trace
 
 ```bash
-code_search --format toon reverse-trace Ecto.Repo insert --depth 10
+code_search --format toon code reverse-trace Ecto.Repo insert --depth 10
 ```
 
 ## Understanding the Output
@@ -37,7 +37,7 @@ This reveals the call chain: `__catch__ → instrument_render_and_send → rende
 ## Use Case: Finding Entry Points
 
 ```bash
-code_search --format toon reverse-trace MyApp.Repo get --depth 8
+code_search --format toon code reverse-trace MyApp.Repo get --depth 8
 ```
 
 Traces backward to find all controller actions or API endpoints that eventually call `Repo.get`.
diff --git a/templates/skills/search/skill.md b/templates/skills/search/skill.md
index 96b1ce5..8159da8 100644
--- a/templates/skills/search/skill.md
+++ b/templates/skills/search/skill.md
@@ -3,7 +3,7 @@
 ## Find Modules by Name
 
 ```bash
-code_search --format toon search Phoenix
+code_search --format toon code search Phoenix
 ```
 
 Output:
@@ -20,7 +20,7 @@ modules[69]{name,source}:
 ## Find Functions by Pattern
 
 ```bash
-code_search --format toon search render --kind functions
+code_search --format toon code search render --kind functions
 ```
 
 Output:
@@ -34,7 +34,7 @@ functions[12]{arity,module,name,return_type}:
 ## Regex Search for Module Prefix
 
 ```bash
-code_search --format toon search '^Phoenix\.Channel' --regex
+code_search --format toon code search '^Phoenix\.Channel' --regex
 ```
 
 Output:
@@ -48,7 +48,7 @@ modules[3]{name,source}:
 ## Search with Limit
 
 ```bash
-code_search --format toon search Controller --limit 5
+code_search --format toon code search Controller --limit 5
 ```
 
 ## Options Reference
diff --git a/templates/skills/struct-usage/SKILL.md b/templates/skills/struct-usage/SKILL.md
index b8ab9bc..56d421d 100644
--- a/templates/skills/struct-usage/SKILL.md
+++ b/templates/skills/struct-usage/SKILL.md
@@ -14,7 +14,7 @@ Find all functions that work with a specific struct type, either as input parame
 ## Usage
 
 ```bash
-code_search --format toon struct-usage <PATTERN> [MODULE] [OPTIONS]
+code_search --format toon code struct-usage <PATTERN> [MODULE] [OPTIONS]
 ```
 
 ## Arguments
@@ -35,11 +35,11 @@ code_search --format toon struct-usage <PATTERN> [MODULE] [OPTIONS]
 ## Examples
 
 ```bash
-code_search struct-usage "User.t"             # Find functions using User.t
-code_search struct-usage "Changeset.t"        # Find functions using Changeset.t
-code_search struct-usage "User.t" MyApp       # Filter to module MyApp
-code_search struct-usage "User.t" --by-module # Summarize by module
-code_search struct-usage -r ".*\.t"           # Regex pattern matching
+code_search code struct-usage "User.t"             # Find functions using User.t
+code_search code struct-usage "Changeset.t"        # Find functions using Changeset.t
+code_search code struct-usage "User.t" MyApp       # Filter to module MyApp
+code_search code struct-usage "User.t" --by-module # Summarize by module
+code_search code struct-usage -r ".*\.t"           # Regex pattern matching
 ```
 
 ## Output Fields (toon format)
diff --git a/templates/skills/trace/skill.md b/templates/skills/trace/skill.md
index b4a950a..a34bb80 100644
--- a/templates/skills/trace/skill.md
+++ b/templates/skills/trace/skill.md
@@ -3,7 +3,7 @@
 ## Basic Forward Trace
 
 ```bash
-code_search --format toon trace Phoenix.Endpoint.RenderErrors "__catch__" --depth 3
+code_search --format toon code trace Phoenix.Endpoint.RenderErrors "__catch__" --depth 3
 ```
 
 Output:
@@ -18,13 +18,13 @@ calls[N]{callee_arity,callee_function,callee_module,caller_function,caller_kind,
 ## Deeper Traversal
 
 ```bash
-code_search --format toon trace MyApp.Web index --depth 10
+code_search --format toon code trace MyApp.Web index --depth 10
 ```
 
 ## Trace with Arity Filter
 
 ```bash
-code_search --format toon trace Phoenix.Controller render --arity 2 --depth 3
+code_search --format toon code trace Phoenix.Controller render --arity 2 --depth 3
 ```
 
 ## Understanding Depth
@@ -38,7 +38,7 @@ Each level shows what gets called at that depth in the call chain.
 ## Use Case: Understanding Error Handling
 
 ```bash
-code_search --format toon trace Phoenix.Endpoint.RenderErrors "__catch__" --depth 5
+code_search --format toon code trace Phoenix.Endpoint.RenderErrors "__catch__" --depth 5
 ```
 
 This reveals the full error handling pipeline: catch → instrument → render → controller.
diff --git a/templates/skills/unused/skill.md b/templates/skills/unused/skill.md
index 1b25a44..98af9b9 100644
--- a/templates/skills/unused/skill.md
+++ b/templates/skills/unused/skill.md
@@ -3,7 +3,7 @@
 ## Find All Unused Functions
 
 ```bash
-code_search --format toon unused
+code_search --format toon code unused
 ```
 
 Output:
@@ -19,7 +19,7 @@ functions[10]{arity,file,kind,line,module,name,project}:
 ## Find Unused Public Functions
 
 ```bash
-code_search --format toon unused -P
+code_search --format toon code unused -P
 ```
 
 These are potential entry points or dead API surface.
@@ -27,7 +27,7 @@ These are potential entry points or dead API surface.
 ## Find Orphan Private Functions
 
 ```bash
-code_search --format toon unused -p
+code_search --format toon code unused -p
 ```
 
 Private functions that are never called are definitely dead code.
@@ -35,7 +35,7 @@ Private functions that are never called are definitely dead code.
 ## Exclude Generated Functions
 
 ```bash
-code_search --format toon unused -Px
+code_search --format toon code unused -Px
 ```
 
 Filters out `__struct__`, `__using__`, `__before_compile__`, etc.
@@ -43,7 +43,7 @@ Filters out `__struct__`, `__using__`, `__before_compile__`, etc.
 ## Filter to Specific Module
 
 ```bash
-code_search --format toon unused MyApp.Accounts
+code_search --format toon code unused MyApp.Accounts
 ```
 
 ## Understanding Results
diff --git a/templates/skills/workflows/code-quality-audit.md b/templates/skills/workflows/code-quality-audit.md
index 2841f84..8774af9 100644
--- a/templates/skills/workflows/code-quality-audit.md
+++ b/templates/skills/workflows/code-quality-audit.md
@@ -26,13 +26,13 @@ Systematically assess codebase health by identifying architectural issues, compl
 Cycles create maintenance nightmares:
 ```bash
 # Find all circular dependencies
-code_search --format toon cycles
+code_search --format toon code cycles
 
 # Limit to shorter cycles (more problematic)
-code_search --format toon cycles --max-length 3
+code_search --format toon code cycles --max-length 3
 
 # Check if a specific module is involved in cycles
-code_search --format toon cycles --involving MyApp.Core
+code_search --format toon code cycles --involving MyApp.Core
 ```
 
 **Red flags**: Any cycles, especially short ones (2-3 modules).
@@ -42,13 +42,13 @@ code_search --format toon cycles --involving MyApp.Core
 Modules doing too much:
 ```bash
 # Find modules with many functions and high connectivity
-code_search --format toon god-modules
+code_search --format toon code god-modules
 
 # Adjust thresholds for your codebase
-code_search --format toon god-modules --min-functions 30 --min-total 20
+code_search --format toon code god-modules --min-functions 30 --min-total 20
 
 # Filter to specific namespace
-code_search --format toon god-modules MyApp.Core
+code_search --format toon code god-modules MyApp.Core
 ```
 
 **Red flags**: Modules with 50+ functions or 30+ total connections.
@@ -58,16 +58,16 @@ code_search --format toon god-modules MyApp.Core
 Functions that are hard to understand:
 ```bash
 # Find functions with high complexity scores
-code_search --format toon complexity --min 10
+code_search --format toon code complexity --min 10
 
 # Find deeply nested functions
-code_search --format toon complexity --min-depth 4
+code_search --format toon code complexity --min-depth 4
 
 # Find large functions by line count
-code_search --format toon large-functions --min-lines 50
+code_search --format toon code large-functions --min-lines 50
 
 # Find functions with many pattern-match clauses
-code_search --format toon many-clauses --min-clauses 8
+code_search --format toon code many-clauses --min-clauses 8
 ```
 
 **Red flags**: Complexity > 15, nesting > 4, lines > 100, clauses > 10.
@@ -77,13 +77,13 @@ code_search --format toon many-clauses --min-clauses 8
 Find over-connected code:
 ```bash
 # Most called functions (might be over-used)
-code_search --format toon hotspots --kind incoming -l 20
+code_search --format toon code hotspots --kind incoming -l 20
 
 # Functions that call too many things (god functions)
-code_search --format toon hotspots --kind outgoing -l 20
+code_search --format toon code hotspots --kind outgoing -l 20
 
 # Total connectivity hotspots
-code_search --format toon hotspots --kind total -l 20
+code_search --format toon code hotspots --kind total -l 20
 ```
 
 **Red flags**: Functions with > 20 incoming or > 10 outgoing calls.
@@ -93,14 +93,14 @@ code_search --format toon hotspots --kind total -l 20
 Verify layer separation:
 ```bash
 # Find boundary modules (high fan-in, low fan-out)
-code_search --format toon boundaries
+code_search --format toon code boundaries
 
 # Analyze module clusters
-code_search --format toon clusters --show-dependencies
+code_search --format toon code clusters --show-dependencies
 
 # Check a specific module's position
-code_search --format toon depends-on MyApp.Web.UserController
-code_search --format toon depended-by MyApp.Web.UserController
+code_search --format toon code depends-on MyApp.Web.UserController
+code_search --format toon code depended-by MyApp.Web.UserController
 ```
 
 **Red flags**: Controllers depending on many modules, data layer with high fan-out.
@@ -110,16 +110,16 @@ code_search --format toon depended-by MyApp.Web.UserController
 Code that can be removed:
 ```bash
 # Unused functions
-code_search --format toon unused -x
+code_search --format toon code unused -x
 
 # Focus on definitely-dead private functions
-code_search --format toon unused -px
+code_search --format toon code unused -px
 
 # Find duplicated code
-code_search --format toon duplicates
+code_search --format toon code duplicates
 
 # Modules with most duplication
-code_search --format toon duplicates --by-module
+code_search --format toon code duplicates --by-module
 ```
 
 **Red flags**: > 5% unused functions, significant duplication.
@@ -131,31 +131,31 @@ Run all checks and compile results:
 ```bash
 # 1. Cycles
 echo "=== CIRCULAR DEPENDENCIES ==="
-code_search --format toon cycles --max-length 4
+code_search --format toon code cycles --max-length 4
 
 # 2. God Modules
 echo "=== GOD MODULES ==="
-code_search --format toon god-modules -l 10
+code_search --format toon code god-modules -l 10
 
 # 3. Complexity
 echo "=== COMPLEX FUNCTIONS ==="
-code_search --format toon complexity --min 10 -l 10
+code_search --format toon code complexity --min 10 -l 10
 
 # 4. Large Functions
 echo "=== LARGE FUNCTIONS ==="
-code_search --format toon large-functions --min-lines 75 -l 10
+code_search --format toon code large-functions --min-lines 75 -l 10
 
 # 5. Coupling Hotspots
 echo "=== COUPLING HOTSPOTS ==="
-code_search --format toon hotspots --kind total -l 10
+code_search --format toon code hotspots --kind total -l 10
 
 # 6. Unused Code
 echo "=== UNUSED CODE ==="
-code_search --format toon unused -px -l 20
+code_search --format toon code unused -px -l 20
 
 # 7. Duplicates
 echo "=== DUPLICATES ==="
-code_search --format toon duplicates -l 10
+code_search --format toon code duplicates -l 10
 ```
 
 ## Interpreting Results
diff --git a/templates/skills/workflows/find-dead-code.md b/templates/skills/workflows/find-dead-code.md
index a281225..e8f4d45 100644
--- a/templates/skills/workflows/find-dead-code.md
+++ b/templates/skills/workflows/find-dead-code.md
@@ -25,13 +25,13 @@ Identify and safely remove unused code to reduce maintenance burden and improve
 Private functions that are never called are guaranteed dead:
 ```bash
 # Find all unused private functions
-code_search --format toon unused -p
+code_search --format toon code unused -p
 
 # Exclude compiler-generated functions
-code_search --format toon unused -px
+code_search --format toon code unused -px
 
 # Filter to specific area
-code_search --format toon unused -p MyApp.Legacy
+code_search --format toon code unused -p MyApp.Legacy
 ```
 
 **These are safe to delete** - private functions can only be called from within their module.
@@ -41,10 +41,10 @@ code_search --format toon unused -p MyApp.Legacy
 Public functions might be called from external code:
 ```bash
 # Find unused public functions
-code_search --format toon unused -P
+code_search --format toon code unused -P
 
 # Exclude generated functions (__struct__, __info__, etc.)
-code_search --format toon unused -Px
+code_search --format toon code unused -Px
 ```
 
 **Before deleting**, verify:
@@ -58,7 +58,7 @@ code_search --format toon unused -Px
 Modules with no incoming dependencies might be dead:
 ```bash
 # For each suspicious module, check dependents
-code_search --format toon depended-by MyApp.OldFeature
+code_search --format toon code depended-by MyApp.OldFeature
 
 # If result shows 0 dependents and not a known entry point, likely dead
 ```
@@ -75,10 +75,10 @@ Common false positives:
 Code that's duplicated might indicate dead or consolidatable functions:
 ```bash
 # Find duplicate implementations
-code_search --format toon duplicates
+code_search --format toon code duplicates
 
 # See which modules have most duplication
-code_search --format toon duplicates --by-module
+code_search --format toon code duplicates --by-module
 ```
 
 ### 5. Validate Before Deleting
@@ -86,10 +86,10 @@ code_search --format toon duplicates --by-module
 For each candidate:
 ```bash
 # Double-check no callers
-code_search --format toon calls-to ModuleName function_name
+code_search --format toon code calls-to ModuleName function_name
 
 # Check if it's a boundary/entry point
-code_search --format toon hotspots ModuleName
+code_search --format toon code hotspots ModuleName
 # Functions with 0 incoming but called from outside Elixir won't show here
 ```
 
@@ -97,25 +97,25 @@ code_search --format toon hotspots ModuleName
 
 ```bash
 # 1. Find all unused functions in legacy area
-code_search --format toon unused MyApp.Legacy
+code_search --format toon code unused MyApp.Legacy
 
 # Result shows 12 unused functions:
 # - 8 private (defp) - safe to delete
 # - 4 public (def) - need verification
 
 # 2. Check the private functions
-code_search --format toon unused -p MyApp.Legacy
+code_search --format toon code unused -p MyApp.Legacy
 # Confirmed: 8 private functions never called
 
 # 3. For each public function, verify
-code_search --format toon calls-to MyApp.Legacy old_helper
+code_search --format toon code calls-to MyApp.Legacy old_helper
 # 0 callers - can delete
 
-code_search --format toon calls-to MyApp.Legacy format_data
+code_search --format toon code calls-to MyApp.Legacy format_data
 # 0 internal callers, but check if it's API
 
 # 4. Check if the whole module is orphaned
-code_search --format toon depended-by MyApp.Legacy
+code_search --format toon code depended-by MyApp.Legacy
 # 0 dependents - entire module might be deletable
 
 # 5. Safe to remove:
diff --git a/templates/skills/workflows/impact-analysis.md b/templates/skills/workflows/impact-analysis.md
index d7d8b5b..236b6ce 100644
--- a/templates/skills/workflows/impact-analysis.md
+++ b/templates/skills/workflows/impact-analysis.md
@@ -24,10 +24,10 @@ Be specific about the change:
 Start with immediate impact:
 ```bash
 # Who calls this function directly?
-code_search --format toon calls-to MyApp.Payments charge
+code_search --format toon code calls-to MyApp.Payments charge
 
 # For a specific arity
-code_search --format toon calls-to MyApp.Payments charge 2
+code_search --format toon code calls-to MyApp.Payments charge 2
 ```
 
 ### 3. Find Transitive Callers
@@ -35,10 +35,10 @@ code_search --format toon calls-to MyApp.Payments charge 2
 Changes propagate up the call chain:
 ```bash
 # Trace backwards to find all paths to this function
-code_search --format toon reverse-trace MyApp.Payments charge --depth 5
+code_search --format toon code reverse-trace MyApp.Payments charge --depth 5
 
 # Increase depth for widely-used functions
-code_search --format toon reverse-trace MyApp.Repo insert --depth 10
+code_search --format toon code reverse-trace MyApp.Repo insert --depth 10
 ```
 
 ### 4. Check Module-Level Impact
@@ -46,10 +46,10 @@ code_search --format toon reverse-trace MyApp.Repo insert --depth 10
 For broader changes, check module dependencies:
 ```bash
 # What modules depend on this one?
-code_search --format toon depended-by MyApp.Payments
+code_search --format toon code depended-by MyApp.Payments
 
 # Check if any of those are also widely used
-code_search --format toon depended-by MyApp.PaymentsWeb
+code_search --format toon code depended-by MyApp.PaymentsWeb
 ```
 
 ### 5. Assess Type-Level Impact
@@ -57,13 +57,13 @@ code_search --format toon depended-by MyApp.PaymentsWeb
 If changing types or structs:
 ```bash
 # Who uses this type?
-code_search --format toon struct-usage Payment.t
+code_search --format toon code struct-usage Payment.t
 
 # Who accepts this type?
-code_search --format toon accepts Payment.t
+code_search --format toon code accepts Payment.t
 
 # Who returns this type?
-code_search --format toon returns Payment.t
+code_search --format toon code returns Payment.t
 ```
 
 ### 6. Check for Boundary Crossings
@@ -71,10 +71,10 @@ code_search --format toon returns Payment.t
 See if the change affects architectural boundaries:
 ```bash
 # Is this a boundary module (many callers, few dependencies)?
-code_search --format toon boundaries MyApp.Payments
+code_search --format toon code boundaries MyApp.Payments
 
 # Check cluster membership
-code_search --format toon clusters MyApp.Payments
+code_search --format toon code clusters MyApp.Payments
 ```
 
 Changes to boundary modules have wider impact.
@@ -84,15 +84,15 @@ Changes to boundary modules have wider impact.
 Get concrete numbers:
 ```bash
 # Count callers
-code_search --format toon calls-to MyApp.Payments charge
+code_search --format toon code calls-to MyApp.Payments charge
 # Look at the count in output
 
 # Count dependent modules
-code_search --format toon depended-by MyApp.Payments
+code_search --format toon code depended-by MyApp.Payments
 # Look at the count in output
 
 # Check hotspot status
-code_search --format toon hotspots MyApp.Payments
+code_search --format toon code hotspots MyApp.Payments
 # High incoming = high impact
 ```
 
@@ -102,19 +102,19 @@ You want to change `MyApp.Accounts.get_user/1` to `get_user/2` (adding options):
 
 ```bash
 # 1. Find direct callers
-code_search --format toon calls-to MyApp.Accounts get_user
+code_search --format toon code calls-to MyApp.Accounts get_user
 # Result: 15 direct callers
 
 # 2. Trace backwards
-code_search --format toon reverse-trace MyApp.Accounts get_user --depth 4
+code_search --format toon code reverse-trace MyApp.Accounts get_user --depth 4
 # Result: Shows call chains from controllers, jobs, other contexts
 
 # 3. Check module impact
-code_search --format toon depended-by MyApp.Accounts
+code_search --format toon code depended-by MyApp.Accounts
 # Result: 8 modules depend on Accounts
 
 # 4. See if it's a hotspot
-code_search --format toon hotspots MyApp.Accounts
+code_search --format toon code hotspots MyApp.Accounts
 # Result: get_user has 15 incoming calls - medium impact
 
 # Conclusion: Need to update 15 call sites across 8 modules
@@ -126,18 +126,18 @@ You want to remove `MyApp.LegacyPayments`:
 
 ```bash
 # 1. Check if anything depends on it
-code_search --format toon depended-by MyApp.LegacyPayments
+code_search --format toon code depended-by MyApp.LegacyPayments
 # Result: 0 dependents - safe to delete!
 
 # Or if there are dependents:
 # Result: 3 modules still depend on it
 
 # 2. Find specific usages
-code_search --format toon calls-to MyApp.LegacyPayments
+code_search --format toon code calls-to MyApp.LegacyPayments
 # Shows exactly which functions are still called
 
 # 3. Check for type usage
-code_search --format toon struct-usage LegacyPayment.t
+code_search --format toon code struct-usage LegacyPayment.t
 # Shows if the struct is still used anywhere
 ```
 
diff --git a/templates/skills/workflows/trace-execution-flow.md b/templates/skills/workflows/trace-execution-flow.md
index eac84e1..7052387 100644
--- a/templates/skills/workflows/trace-execution-flow.md
+++ b/templates/skills/workflows/trace-execution-flow.md
@@ -22,13 +22,13 @@ Entry points are typically:
 Find potential entry points:
 ```bash
 # Find controller actions
-code_search --format toon search Controller --kind modules
+code_search --format toon code search Controller --kind modules
 
 # Browse a controller to find actions
-code_search --format toon browse-module MyApp.UserController
+code_search --format toon code browse-module MyApp.UserController
 
 # Find GenServer callbacks
-code_search --format toon location handle_call
+code_search --format toon code location handle_call
 ```
 
 ### 2. Trace Forward from Entry Point
@@ -36,10 +36,10 @@ code_search --format toon location handle_call
 Use `trace` to follow the call chain:
 ```bash
 # Trace 5 levels deep (default)
-code_search --format toon trace MyApp.UserController create
+code_search --format toon code trace MyApp.UserController create
 
 # Trace deeper for complex flows
-code_search --format toon trace MyApp.UserController create --depth 10
+code_search --format toon code trace MyApp.UserController create --depth 10
 ```
 
 **Reading the output:**
@@ -52,17 +52,17 @@ code_search --format toon trace MyApp.UserController create --depth 10
 When you see an interesting callee, dive deeper:
 ```bash
 # What does this specific function call?
-code_search --format toon calls-from MyApp.Accounts create_user
+code_search --format toon code calls-from MyApp.Accounts create_user
 
 # Continue tracing from there
-code_search --format toon trace MyApp.Accounts create_user --depth 5
+code_search --format toon code trace MyApp.Accounts create_user --depth 5
 ```
 
 ### 4. Find the Path Between Two Points
 
 If you know the start and end:
 ```bash
-code_search --format toon path \
+code_search --format toon code path \
   --from-module MyApp.UserController --from-function create \
   --to-module MyApp.Repo --to-function insert
 ```
@@ -74,23 +74,23 @@ This shows exactly how the controller action reaches the database.
 Sometimes it's useful to trace backwards:
 ```bash
 # Who calls this low-level function?
-code_search --format toon reverse-trace MyApp.Repo insert --depth 3
+code_search --format toon code reverse-trace MyApp.Repo insert --depth 3
 
 # Find all callers (single level)
-code_search --format toon calls-to MyApp.Repo insert
+code_search --format toon code calls-to MyApp.Repo insert
 ```
 
 ## Example: Tracing a User Registration Flow
 
 ```bash
 # 1. Find the registration controller
-code_search --format toon search Registration
+code_search --format toon code search Registration
 
 # 2. Browse the controller
-code_search --format toon browse-module MyApp.RegistrationController
+code_search --format toon code browse-module MyApp.RegistrationController
 
 # 3. Trace from the create action
-code_search --format toon trace MyApp.RegistrationController create --depth 8
+code_search --format toon code trace MyApp.RegistrationController create --depth 8
 
 # 4. Output reveals the flow:
 #    Controller.create
diff --git a/templates/skills/workflows/understand-feature.md b/templates/skills/workflows/understand-feature.md
index 6167992..67be6f7 100644
--- a/templates/skills/workflows/understand-feature.md
+++ b/templates/skills/workflows/understand-feature.md
@@ -16,12 +16,12 @@ Build a complete mental model of a feature by exploring it vertically through al
 Start by searching for related modules:
 ```bash
 # Search by feature name
-code_search --format toon search Payment
-code_search --format toon search Billing
-code_search --format toon search Subscription
+code_search --format toon code search Payment
+code_search --format toon code search Billing
+code_search --format toon code search Subscription
 
 # Search with regex for related patterns
-code_search --format toon search '^MyApp\.Payments' --regex
+code_search --format toon code search '^MyApp\.Payments' --regex
 ```
 
 ### 2. Identify the Core Module
@@ -29,12 +29,12 @@ code_search --format toon search '^MyApp\.Payments' --regex
 Usually there's a central module that orchestrates the feature:
 ```bash
 # Browse candidate modules
-code_search --format toon browse-module MyApp.Payments
-code_search --format toon browse-module MyApp.Billing
+code_search --format toon code browse-module MyApp.Payments
+code_search --format toon code browse-module MyApp.Billing
 
 # Check which one has more connections (likely the core)
-code_search --format toon depended-by MyApp.Payments
-code_search --format toon depended-by MyApp.Billing
+code_search --format toon code depended-by MyApp.Payments
+code_search --format toon code depended-by MyApp.Billing
 ```
 
 The module with more dependents is often the public API of the feature.
@@ -44,13 +44,13 @@ The module with more dependents is often the public API of the feature.
 Understand what the core module provides:
 ```bash
 # See all public functions
-code_search --format toon browse-module MyApp.Payments --kind functions
+code_search --format toon code browse-module MyApp.Payments --kind functions
 
 # See type definitions
-code_search --format toon browse-module MyApp.Payments --kind types
+code_search --format toon code browse-module MyApp.Payments --kind types
 
 # See struct definitions
-code_search --format toon browse-module MyApp.Payments --kind structs
+code_search --format toon code browse-module MyApp.Payments --kind structs
 ```
 
 ### 4. Explore Upward (Who Uses This Feature?)
@@ -58,13 +58,13 @@ code_search --format toon browse-module MyApp.Payments --kind structs
 Find the entry points and consumers:
 ```bash
 # What modules depend on this feature?
-code_search --format toon depended-by MyApp.Payments
+code_search --format toon code depended-by MyApp.Payments
 
 # Find specific callers of key functions
-code_search --format toon calls-to MyApp.Payments process_payment
+code_search --format toon code calls-to MyApp.Payments process_payment
 
 # Trace backwards to find entry points
-code_search --format toon reverse-trace MyApp.Payments process_payment --depth 5
+code_search --format toon code reverse-trace MyApp.Payments process_payment --depth 5
 ```
 
 This reveals:
@@ -77,10 +77,10 @@ This reveals:
 Find the dependencies:
 ```bash
 # What does this module depend on?
-code_search --format toon depends-on MyApp.Payments
+code_search --format toon code depends-on MyApp.Payments
 
 # Trace forward from key functions
-code_search --format toon trace MyApp.Payments process_payment --depth 5
+code_search --format toon code trace MyApp.Payments process_payment --depth 5
 ```
 
 This reveals:
@@ -93,11 +93,11 @@ This reveals:
 Understand what data types flow through the feature:
 ```bash
 # What functions accept the main struct?
-code_search --format toon struct-usage Payment.t
+code_search --format toon code struct-usage Payment.t
 
 # Or search by type pattern
-code_search --format toon accepts Payment
-code_search --format toon returns Payment
+code_search --format toon code accepts Payment
+code_search --format toon code returns Payment
 ```
 
 ### 7. Check for Related Background Processing
@@ -105,40 +105,40 @@ code_search --format toon returns Payment
 Features often have async components:
 ```bash
 # Find related workers/jobs
-code_search --format toon search PaymentWorker
-code_search --format toon search 'Payment.*Job' --regex
+code_search --format toon code search PaymentWorker
+code_search --format toon code search 'Payment.*Job' --regex
 
 # Find GenServer patterns
-code_search --format toon search PaymentServer
+code_search --format toon code search PaymentServer
 ```
 
 ## Example: Understanding the Authentication Feature
 
 ```bash
 # 1. Find auth-related modules
-code_search --format toon search Auth
+code_search --format toon code search Auth
 # Found: MyApp.Auth, MyApp.Auth.Guardian, MyApp.Auth.Pipeline
 
 # 2. Browse the main module
-code_search --format toon browse-module MyApp.Auth
+code_search --format toon code browse-module MyApp.Auth
 # Shows: authenticate/2, register/1, verify_token/1, etc.
 
 # 3. Who uses auth?
-code_search --format toon depended-by MyApp.Auth
+code_search --format toon code depended-by MyApp.Auth
 # Found: SessionController, ApiController, all protected controllers
 
 # 4. What does auth depend on?
-code_search --format toon depends-on MyApp.Auth
+code_search --format toon code depends-on MyApp.Auth
 # Found: Repo, Guardian, Comeonin
 
 # 5. Trace a key flow
-code_search --format toon trace MyApp.Auth authenticate --depth 5
+code_search --format toon code trace MyApp.Auth authenticate --depth 5
 # Shows: authenticate → verify_password → Comeonin.check_pass
 #                     → load_user → Repo.get_by
 #                     → create_token → Guardian.encode_and_sign
 
 # 6. Map the user data flow
-code_search --format toon struct-usage User.t MyApp.Auth
+code_search --format toon code struct-usage User.t MyApp.Auth
 ```
 
 ## Building the Mental Model