Gate tool calls per command and path, not per tool name

Approval was a list of tool names: `bash` needed it, `read_file` did not. That
fails in a specific way. `bash` covers `git status` and `rm -rf` equally, so a
user working through a batch presses `a` — always allow — on the first prompt and
every later command runs unasked, including the one they would have refused. The
gate was strongest when it mattered least and gone by the time it mattered.

Rules now match the *subject* of a call: the command for `bash`, the path for a
file tool, the pattern for a search.

    "permission": {
      "bash": { "*": "ask", "git *": "allow", "rm *": "deny" },
      "edit_file": { "*": "deny", "src/generated/*": "allow" }
    }

Plain last-match-wins, with no special case for deny. An earlier version made
deny win wherever it sat, on the theory that a refusal should be impossible to
undo by accident, and it made default-deny-with-exceptions unexpressible — which
is the shape a careful user actually writes, and the same shape as `*.env` denied
while `*.env.example` is allowed. Refusals that must never be configurable stay
in the guard plugin, which runs ahead of this and which --yolo cannot reach.

Three behaviours fall out of it:

- `always` grants the pattern the tool suggests, not the tool. Approving
  `git status` runs `git log` unprompted and still asks about `npm publish`.
- `.env`, `.env.*`, and `.pem` are denied on read by default. Not gated, refused:
  a secret that reaches the context is on the wire and in the session file, and
  there is no taking it back. `.env.example` stays allowed.
- A call repeated identically three times in one turn asks even when allowed. A
  model repeating itself is not making progress, and `bash: allow` is a statement
  about which commands are safe rather than permission to loop.

The prompt now says which rule matched and what `always` would grant:

    bash wants to run
    git status --porcelain
    y allow once | a always allow bash git * | n deny

A typo in a decision string is dropped at parse time, leaving the tool on its
default. Treating an unparseable value as `allow` would mean one misspelling
silently removing the gate.

Written after surveying Claude Code, Codex, opencode, and phi. Three of the four
had already moved to per-pattern rules; the credential deny and the repeat guard
come from opencode directly. ROADMAP records what was deliberately not taken and
why — OS sandboxing needs three platform implementations and is worse than
nothing if half-built, and opencode's own docs say LSP integration is often not a
net positive.

581 tests, up from 572. The engine is a pure function tested on its own, and the
loop is tested through a real Session: an allowed pattern never prompts, a denied
one never executes, and a `.env` read leaves no secret in the transcript.

docs/configuration.md

@@ -22,6 +22,9 @@ Written by `/provider`, editable by hand. Every field is optional.
   "maxRetries": 3,
   "plugins": ["guard", "time"],
   "toolSets": ["edit-plus", "git"],
+  "permission": {
+    "bash": { "*": "ask", "git *": "allow" }
+  },
   "registryUrl": "https://example.com/my-registry/index.json",
   "mcpServers": {
     "fs": { "command": "npx", "args": ["-y", "@modelcontextprotocol/server-filesystem", "."] }
@@ -41,6 +44,7 @@ Written by `/provider`, editable by hand. Every field is optional.
 | `maxRetries` | retries per model call for transient failures. Default 3 |
 | `plugins` | which builtin plugins to enable. Omit for `["guard", "time"]` |
 | `toolSets` | optional tool sets beyond `core`: `edit-plus`, `git`. Omit for all of them. See [tools](tools.md) |
+| `permission` | which calls run, ask, or are refused, matched per command or path. See [permissions](permissions.md) |
 | `registryUrl` | index for `/registry`. Omit for the default. See [registry](registry.md) |
 | `mcpServers` | see [MCP](mcp.md) |
 
@@ -212,7 +216,7 @@ interesting — see [memory](memory.md#the-pruning-repair).
 
 ## Config that changes behaviour subtly
 
-Three fields do more than they look like they do.
+Four fields do more than they look like they do.
 
 **`thinking`** costs money and latency on every turn, not just hard ones. `off` on a hard problem
 produces confident wrong answers; `max` on a rename wastes cents and seconds. The agent variants
@@ -222,6 +226,10 @@ already pick sensible levels — see [agents](agents.md).
 expected, check the startup header for which sets loaded: an unrecognised name is dropped
 silently, so `"gti"` reads as "git is off". See [tools](tools.md#tool-sets).
 
+**`permission`** replaces a tool's defaults rather than merging with them, so
+`{ "read_file": { "*": "allow" } }` also allows reading `.env`. Order inside a rule table decides
+the outcome, since later rules win. See [permissions](permissions.md).
+
 **`registryUrl`** is the whole trust decision for installed skills and plugins. There are no
 signatures, so pointing it at an index means trusting whoever controls that URL — including for
 whatever they publish later. See [registry](registry.md).