Rename system extension layer to base for clarity

Replace all references to the "system" layer with "base" to better reflect
its role as the foundational extension/tool layer in panto's hierarchy.
The layer hierarchy now consistently uses: project > user > base.

Includes:
- Update agent README and build.zig documentation
- Refactor tool registry and config module to support layered lookups
- Add TestHarness abstraction for cleaner test setup
- Improve JSON serialization with wire-encoded tool names
- Add glob pattern matching for tool/extension discovery

1 files changed, 31 insertions, 5 deletions

diff --git a/libpanto/src/openai_chat_json.zig b/libpanto/src/openai_chat_json.zig
index 37d347b..6991559 100644
--- a/libpanto/src/openai_chat_json.zig
+++ b/libpanto/src/openai_chat_json.zig
@@ -117,7 +117,7 @@ pub fn serializeRequest(
     if (tools.count() > 0) {
         try s.objectField("tools");
         try s.beginArray();
-        var it = tools.iterator();
+        var it = tools.toolsForLLM();
         while (it.next()) |t| {
             try s.beginObject();
             try s.objectField("type");
@@ -125,6 +125,7 @@ pub fn serializeRequest(
             try s.objectField("function");
             try s.beginObject();
             try s.objectField("name");
+            // `t.decl.name` is already wire-encoded by `toolsForLLM`.
             try s.write(t.decl.name);
             try s.objectField("description");
             try s.write(t.decl.description);
@@ -261,7 +262,11 @@ fn writeMessage(s: *std.json.Stringify, msg: conversation.Message, allocator: Al
                 try s.objectField("function");
                 try s.beginObject();
                 try s.objectField("name");
-                try s.write(tu.name);
+                // Replayed assistant tool_use. The conversation stores the
+                // internal (dotted) name; encode `.` -> `__` so it matches
+                // what we advertise in `tools`.
+                var name_buf: [tool_registry_mod.max_wire_name_len]u8 = undefined;
+                try s.write(tool_registry_mod.encodeName(&name_buf, tu.name));
                 try s.objectField("arguments");
                 // `arguments` is a string carrying JSON, per the OpenAI
                 // wire format — not a nested object.
@@ -664,9 +669,7 @@ test "serializeRequest - emits tools array when registry non-empty" {
     var tools = emptyTools();
     defer tools.deinit();
 
-    try tools.register(makeStaticTool(
-        "echo",
-        "Echo a message back.",
+    try tools.register(makeStaticTool("echo", "Echo a message back.",
         \\{"type":"object","properties":{"message":{"type":"string"}},"required":["message"]}
     ));
 
@@ -691,6 +694,29 @@ test "serializeRequest - emits tools array when registry non-empty" {
     try testing.expect(params.get("required").? == .array);
 }
 
+test "serializeRequest - dotted tool name is wire-encoded with __" {
+    const allocator = testing.allocator;
+
+    var conv = conversation.Conversation.init(allocator);
+    defer conv.deinit();
+    try conv.addUserMessage("go");
+
+    var tools = emptyTools();
+    defer tools.deinit();
+    try tools.register(makeStaticTool("std.read", "Read a file.", "{\"type\":\"object\"}"));
+
+    const cfg = testConfig("gpt-4o");
+    const body = try serializeRequest(allocator, &cfg, &conv, &tools);
+    defer allocator.free(body);
+
+    var parsed = try std.json.parseFromSlice(std.json.Value, allocator, body, .{});
+    defer parsed.deinit();
+
+    const f = parsed.value.object.get("tools").?.array.items[0].object.get("function").?.object;
+    // Internal `std.read` crosses the wire as `std__read` (OpenAI forbids dots).
+    try testing.expectEqualStrings("std__read", f.get("name").?.string);
+}
+
 test "serializeRequest - assistant ToolUse becomes tool_calls" {
     const allocator = testing.allocator;