Update README to enhance documentation on secrets run functionality and improve diagram formatting

- Replaced static diagram with a mermaid flowchart for better visualization of secrets management.
- Expanded section on `secrets run` to clarify its operation as a pull → run → clear pipeline.
- Added examples and syntax details for using `secrets run` in various scenarios.
- Included information on automatic clearing of plaintext files after command execution.

README.md

@@ -16,13 +16,28 @@ People end up sharing secrets over Slack, email, or sticky notes. When a key cha
 
 `secrets` encrypts your secret files and stores them in a separate, private git repository. Only someone with the encryption key can read them.
 
-```diagram
-Your project (e.g. ~/myapp/)           Your secrets store (~/.secrets/)
-┌──────────────────────────┐          ┌──────────────────────────┐
-│ .env          (plaintext)│──encrypt─▶│ myapp/.env.age (encrypted)│──sync──▶ GitHub (private)
-│ .env.staging  (plaintext)│          │ myapp/.env.staging.age    │
-│ .dev.vars     (plaintext)│          │ key.txt (never uploaded)  │
-└──────────────────────────┘          └──────────────────────────┘
+```mermaid
+flowchart TD
+    subgraph project["Your project (~/myapp/)"]
+        direction TB
+        p1[".env (plaintext)"]
+        p2[".env.staging (plaintext)"]
+        p3[".dev.vars (plaintext)"]
+    end
+
+    subgraph store["Your secrets store (~/.secrets/)"]
+        direction TB
+        s1["myapp/.env.age (encrypted)"]
+        s2["myapp/.env.staging.age"]
+        k["key.txt (never uploaded)"]
+    end
+
+    gh["GitHub (private)"]
+
+    project -->|secrets push<br/>encrypt| store
+    store -->|git push| gh
+    gh -->|git pull| store
+    store -->|secrets pull<br/>decrypt| project
 ```
 
 - **Encrypted at rest** — files are encrypted with [age](https://github.com/FiloSottile/age), a modern encryption tool. Without the key, the files are unreadable.
@@ -160,18 +175,41 @@ When you run `secrets push` or `secrets pull` without specifying a project name,
 
 You can also specify a name explicitly: `secrets push myapp`.
 
-### Minimizing plaintext exposure
+### secrets run
 
-Every second that plaintext secret files sit on disk is a window for a compromised tool or dependency to read them. `secrets run` shrinks that window to only while your command is running:
+`secrets run` is a **pull → run → clear** pipeline: it runs `secrets pull` to decrypt the latest files into your project, executes your command, then runs `secrets clear` when that command finishes. Plaintext `.env` / `.dev.vars` files exist only while your command is running.
 
-```bash
-secrets run npm start           # .env exists only while dev server is up
-secrets run wrangler deploy     # .dev.vars exists only during deploy
+That matters because anything on disk can be read by other processes. `secrets run` keeps that window as small as possible—useful for dev servers, deploys, and one-off scripts.
+
+```mermaid
+flowchart TD
+    subgraph run["secrets run"]
+        direction TB
+        A[secrets pull] --> B["Your command"]
+        B --> C[secrets clear]
+    end
 ```
 
-When the command exits — whether normally, from an error, or from Ctrl-C — the plaintext files are automatically deleted.
+`secrets clear` is hooked to **shell exit**, so it runs after **success**, **non-zero exit**, or **Ctrl-C** (SIGINT).
 
-This works in `package.json` scripts too, so your whole team gets the protection automatically:
+**Syntax**
+
+```bash
+secrets run <command> [args...]
+secrets run -w <command> [args...]    # monorepo: all workspaces (needs jq)
+secrets run -- <command>              # if the command starts with -
+```
+
+Use **`--`** when the program you are running begins with a dash so it is not parsed as a `secrets` flag.
+
+**Examples**
+
+```bash
+secrets run npm start              # .env only while the dev server runs
+secrets run wrangler deploy        # .dev.vars only during deploy
+```
+
+**`package.json` scripts** so the whole team gets the same behavior by default:
 
 ```json
 {
@@ -182,7 +220,9 @@ This works in `package.json` scripts too, so your whole team gets the protection
 }
 ```
 
-Now `npm run dev` pulls secrets, starts the dev server, and clears secrets when you stop it.
+Stopping the dev server (or any failing command) ends the process; the `EXIT` trap clears secrets afterward.
+
+If you prefer to keep decrypted files on disk for a long editing session, use `secrets pull` and `secrets clear` manually instead.
 
 ### Monorepo support