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, 2 insertions, 2 deletions

diff --git a/build.zig b/build.zig
index 659638a..4c12865 100644
--- a/build.zig
+++ b/build.zig
@@ -43,7 +43,7 @@ pub fn build(b: *std.Build) void {
 
     // And the in-repo `agent/` tree: bundled into the binary and
     // staged at $PANTO_HOME/agent/ on first run. This is panto's
-    // "system" extension/tool layer (read/write/edit/bash etc.).
+    // "base" extension/tool layer (read/write/edit/bash etc.).
     const agent_embed_path = generateAgentEmbed(b);
 
     // Constants module: makes Zig know the Lua and luarocks versions
@@ -314,7 +314,7 @@ fn generateLuarocksEmbed(
 /// Codegen step: walk the in-repo `agent/` tree and emit a Zig module
 /// embedding every file. Bootstrap stages the result under
 /// `$PANTO_HOME/agent/` on first run, where the runtime's extension
-/// loader finds it as the "system" layer (below user and project).
+/// loader finds it as the "base" layer (below user and project).
 ///
 /// Unlike `generateLuarocksEmbed`, the agent tree lives in-repo and
 /// its contents change as we add/edit tools. `addDirectoryArg` on a