docs: synchronize documentation with codebase and fix drift

README.md

@@ -46,7 +46,7 @@ Ready to dive deeper? The README only scratches the surface.
 Head over to the **[Official Documentation](https://protostar.readthedocs.io/en/stable/)** for:
 
 - **Command Reference:** Full flags and capabilities for `init`.
-- **Domain Presets:** Matrices for Scientific, Astrophysics, ML, DSP, and Embedded workflows.
+- **Domain Presets:** Matrices for Scientific, Astrophysics, ML, DSP, Embedded, REST API, and CLI Application workflows.
 - **Configuration & Shell Autocomplete:** Setting up global defaults, CLI autocompletion, and advanced AST overrides.
 - **Architecture Mechanics:** Deep dives into the Orchestrator, Executor, and Manifest lifecycle.
 

docs/getting-started.md

@@ -43,7 +43,7 @@ protostar init
 For rapid, repeatable initialization, you can bypass the TUI entirely by providing your desired environment matrix as CLI flags. Universal system workspace hygiene is automatically applied, and IDE settings are conditionally injected based on your global configuration and chosen language footprints.
 
 ```bash
-protostar init --python --scientific --pytest --markdownlint
+protostar init --scientific --pytest --markdownlint
 ```
 
 **What just happened?**
@@ -55,18 +55,6 @@ In a fraction of a second, Protostar:
 
 ![Headless Scaffolding](../assets/demo_headless.gif){ width="700" }
 
-## Generating Boilerplate
-
-While `init` handles the global repository architecture, the `generate` command handles repetitive, discrete file scaffolding.
-
-```bash
-protostar generate cpp-class TelemetryIngestor
-```
-
-This safely drops a `TelemetryIngestor.hpp` and `TelemetryIngestor.cpp` into your working directory with standard include guards and empty constructors, aborting safely if the files already exist.
-
-![Target Generation](../assets/demo_generate.gif){ width="700" }
-
 ## Exploration & Help
 
 Protostar is self-documenting. You can view the full capabilities matrix and subcommand details directly from your terminal at any time.

docs/index.md

@@ -40,7 +40,7 @@ It is designed to automate environment setup while staying out of your way.
 ```bash
 mkdir orbital-mechanics-sim
 cd orbital-mechanics-sim
-protostar init --python --scientific --pytest --markdownlint
+protostar init --scientific --pytest --markdownlint
 ```
 
 </div>

docs/mechanics/manifest.md

@@ -55,7 +55,7 @@ During the `build()` phase, modules utilize the manifest's unified API to regist
 
 ## State Serialization
 
-To understand the decoupling, it is helpful to visualize the manifest's internal state. Below is a dynamically generated JSON representation of the aggregate state just before execution, simulating a user running `protostar init --python --astro --ruff`.
+To understand the decoupling, it is helpful to visualize the manifest's internal state. Below is a dynamically generated JSON representation of the aggregate state just before execution, simulating a user running `protostar init --astro --ruff`.
 
 --8<-- "manifest_state.md"
 

docs/mechanics/modules.md

@@ -1,6 +1,6 @@
 # The Module Architecture
 
-At its core, Protostar is not a monolithic script; it is a polymorphic module resolution engine. The CLI parser's sole responsibility is translating a matrix of boolean flags (e.g., `--python --astro --ruff`) into an ordered array of instantiated module objects.
+At its core, Protostar is not a monolithic script; it is a polymorphic module resolution engine. The CLI parser's sole responsibility is translating a matrix of boolean flags (e.g., `--astro --ruff`) into an ordered array of instantiated module objects.
 
 These modules act as autonomous, stateless plugins that interact strictly with the `EnvironmentManifest`. They do not know about each other, they do not read the host filesystem, and they do not execute system commands directly.
 

docs/mechanics/orchestrator.md

@@ -117,7 +117,7 @@ The Orchestrator serves as the absolute boundary for exception propagation. By t
 
     - __OS__: Darwin 25.3.0
     - __Python__: 3.14.3
-    - __Command__: `protostar init --python --astro --crash-test`
+    - __Command__: `protostar init --astro --crash-test`
 
     ### Traceback
 

docs/usage/init.md

@@ -28,7 +28,7 @@ To understand how Protostar interprets your flags, observe what happens when we
     The following repository tree examples assume you have explicitly configured an IDE in your global settings (e.g., `ide = "vscode"`) in addition to globally enabling direnv. This represents the best practice configuration for vscode users scaffolding python environments. If your config remains set to the default `None`, the `.vscode/settings.json` file will not be generated, though the universal `.vscode/` exclusion will still be safely appended to your `.gitignore`.
 
 === "The CLI Application (Tooling Focus)"
-    __Command:__ `protostar init --python --cli --mypy --pytest --pre-commit --markdownlint`
+    __Command:__ `protostar init --cli --mypy --pytest --pre-commit --markdownlint`
 
     This footprint demonstrates Protostar's ability to wire complex tooling together automatically.
 
@@ -54,7 +54,7 @@ To understand how Protostar interprets your flags, observe what happens when we
     - **A Note on Speed:** Standard Protostar executions take fractions of a second. However, because `--pre-commit` was flagged, Protostar queued a `pre-commit autoupdate` subprocess at the end of the run to ensure your git hooks are pinned to the absolute latest network releases. This shifts the total execution time to roughly ~4-9 seconds.
 
 === "The Astrophysics Pipeline (Data Focus)"
-    __Command:__ `protostar init --python --astro`
+    __Command:__ `protostar init --astro`
 
     This footprint focuses on managing heavy, serialized data assets and preventing repository bloat.
 
@@ -77,7 +77,7 @@ To understand how Protostar interprets your flags, observe what happens when we
     - **Artifact Exclusions:** The `.gitignore` was populated with `*.fits`, `*.csv`, and `*.parquet`, preventing you from accidentally committing massive telemetry cubes to version control.
 
 === "The Machine Learning Stack (Artifact Focus)"
-    __Command:__ `protostar init --python --ml --docker`
+    __Command:__ `protostar init --ml --docker`
 
     This footprint focuses on containerization and strictly excluding model artifacts.
 
@@ -106,11 +106,11 @@ To understand how Protostar interprets your flags, observe what happens when we
 
 Developers are rightfully terrified of CLI tools that touch their existing configurations. Protostar is engineered specifically to alleviate this anxiety.
 
-Lets say you initialized a machine learning repo yesterday with `protostar init --python --ml --docker`
+Lets say you initialized a machine learning repo yesterday with `protostar init --ml --docker`
 
 But today you remembered you'll be doing quasar analysis, and you want to enforce strict typing with `mypy`
 
-You simply run `protostar init --python --astro --mypy --docker` in that existing directory.
+You simply run `protostar init --astro --mypy --docker` in that existing directory.
 
 Because Protostar detects existing configuration markers (like `pyproject.toml`), it instantly halts the execution and triggers the __Gravitational Anomaly__ intercept prompt:
 

src/protostar/cli.py

@@ -285,7 +285,7 @@ def build_parser() -> argparse.ArgumentParser:
         description="Scaffolds base Python configurations, dependencies, and environment files.",
         formatter_class=ProtoHelpFormatter,
         usage=argparse.SUPPRESS,
-        epilog="[bold]Example:[/bold]\n  protostar init --python --astro --mypy",
+        epilog="[bold]Example:[/bold]\n  protostar init --astro --mypy",
         parents=[base_parser],
     )