docs: explain --dangerously-skip-permissions for users who hesitate at the flag name

Add an info box in getting-started explaining what the -p and
--dangerously-skip-permissions flags do and why they're safe to use
with ralphify's check system. Also fix the project detection table
order in how-it-works to match the actual code evaluation order.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: 2 people

docs/getting-started.md

@@ -53,6 +53,11 @@ args = ["-p", "--dangerously-skip-permissions"]
 prompt = "PROMPT.md"
 ```
 
+!!! info "What does `--dangerously-skip-permissions` do?"
+    Claude Code normally asks for your approval before running shell commands, editing files, or making git commits. The `--dangerously-skip-permissions` flag disables these interactive prompts so the agent can work autonomously without waiting for input. The `-p` flag enables non-interactive ("print") mode, which reads the prompt from stdin instead of opening a chat session.
+
+    This is safe to use when ralphify is the only thing running the agent, because **checks** act as your guardrails — they validate the agent's work after each iteration and feed failures back for the agent to fix.
+
 **`PROMPT.md`** — the prompt that gets piped to the agent each iteration. The default is a generic starting point — you'll customize it next.
 
 ## Step 3: Write your prompt

docs/how-it-works.md

@@ -280,10 +280,12 @@ When you run `ralph init`, ralphify detects your project type by looking for mar
 
 | File found | Detected type |
 |---|---|
-| `pyproject.toml` | Python |
 | `package.json` | Node.js |
+| `pyproject.toml` | Python |
 | `Cargo.toml` | Rust |
 | `go.mod` | Go |
 | None of the above | Generic |
 
+Files are checked in the order shown above. If a project contains multiple manifest files (e.g. both `package.json` and `pyproject.toml`), the first match wins.
+
 The detected type is displayed during init but doesn't currently change the generated configuration. All project types get the same default `ralph.toml` and `PROMPT.md`.