feat(agentic): scope file/command tools to an agent workspace root

Confine the agentic file tools (read_file, write_file, list_files, grep)
to a configured workspace subtree via a lexical path check, and run
run_command with its cwd set to that root. Root comes from state key
"agent_workspace_root" or env NEURON_AGENT_ROOT. When no root is set,
behavior is unchanged (unscoped) for backward compatibility.

Defense-in-depth, NOT a hard boundary: the lexical guard does not resolve
symlinks and cannot stop an arbitrary shell command from cd-ing out of the
root. Real confinement needs runtime support (cwd-locked exec / sandbox-exec
/ chroot) in el_runtime.c.

Compile-checked with elc (darwin arm64); not link/run-gated locally
(darwin elb unavailable). Needs a soul build + smoke test before merge.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

.gitea/workflows/ci.yaml

@@ -91,29 +91,44 @@ jobs:
           echo "El SDK ready"
           /opt/el/dist/platform/elc --version || true
 
+      - name: Generate ELP master declarations header
+        run: |
+          {
+            printf '/* Auto-generated C forward declarations for ELP cross-module calls */\n'
+            printf '#pragma once\n'
+            printf '#include "el_runtime.h"\n'
+            printf '\n'
+            grep -h -E '^(el_val_t|void|int|char\*|const char\*)[[:space:]]+[a-zA-Z_][a-zA-Z0-9_]*[[:space:]]*\(' dist/*.c 2>/dev/null \
+              | grep ';$' | sort -u
+          } > dist/elp-c-decls.h
+          echo "Generated elp-c-decls.h with $(grep -c ';' dist/elp-c-decls.h 2>/dev/null || echo 0) declarations"
+
       - name: Build neuron soul binary
         run: |
           ELB=/opt/el/dist/bin/elb
           ELC=/opt/el/dist/platform/elc
           RUNTIME=/opt/el/runtime
 
-          # Compile all El modules to C via elb.
-          # elb fails at link on Linux (GNU ld rejects duplicate strong symbols that
-          # macOS ld accepts silently) — that's expected and captured with || true.
-          # The important output is dist/soul.c: the El compiler inlines all imported
-          # modules into the entry-point file, so soul.c is a self-contained
-          # translation unit.  We never link the other dist/*.c files — they contain
-          # the same symbols inlined again, plus capability-violation #error guards
-          # that fire when compiled outside the cgi entrypoint.
+          # Compile all El modules to C.
+          # This step will fail at link on Linux: the El compiler inlines imported
+          # modules into each module's .c file, producing duplicate strong symbol
+          # definitions. GNU ld rejects these; macOS ld accepts them silently.
+          # We capture the link failure and re-link manually below.
           $ELB --elc=$ELC --runtime=$RUNTIME/el_runtime.c || true
 
-          # Link only soul.c + the runtime.  No --allow-multiple-definition needed.
+          # Re-link with soul.c listed first so its real main() (from the cgi block)
+          # wins over the stub main()s generated in every other module.
+          # --allow-multiple-definition tells GNU ld to pick the first definition
+          # for each duplicate symbol — safe here because all duplicates are identical
+          # (same El source compiled independently into multiple .c files).
           mkdir -p dist
+          OTHER_C=$(ls dist/*.c | grep -v '/soul\.c$' | sort | tr '\n' ' ')
           cc -O2 -DHAVE_CURL \
             -I$RUNTIME \
-            dist/soul.c \
+            dist/soul.c $OTHER_C \
             $RUNTIME/el_runtime.c \
             -lssl -lcrypto -lcurl -lpthread -lm \
+            -Wl,--allow-multiple-definition \
             -o dist/neuron
 
           ls -lh dist/neuron

chat.el

@@ -377,16 +377,78 @@ fn call_neuron_mcp(tool_name: String, args: String) -> String {
     return json_safe(result)
 }
 
+// ---------------------------------------------------------------------------
+// Agent workspace scope (defense-in-depth, NOT a hard security boundary).
+//
+// When a workspace root is configured (state key "agent_workspace_root", else
+// env NEURON_AGENT_ROOT), the path-based tools (read_file, write_file,
+// list_files, grep) are confined to that subtree by a lexical check, and
+// run_command runs with its cwd set to the root. With no root set, behavior is
+// unchanged (unscoped) for backward compatibility.
+//
+// LIMITATION — FLAGGED FOR WILL'S REVIEW: this is a lexical guard. It does not
+// resolve symlinks and cannot stop an arbitrary shell command from cd-ing out
+// of the root. Real confinement needs runtime support (cwd-locked exec /
+// sandbox-exec / chroot) in el_runtime.c. This raises the floor; it is not a
+// boundary. The default-allow-when-unset policy and the "cd <root> && (...)"
+// wrapping are deliberate choices to confirm against the intended design.
+// ---------------------------------------------------------------------------
+
+fn agent_workspace_root() -> String {
+    let s: String = state_get("agent_workspace_root")
+    if !str_eq(s, "") {
+        return s
+    }
+    return env("NEURON_AGENT_ROOT")
+}
+
+// Allow if path stays under root. Empty root = no sandbox = allow. Rejects
+// parent traversal and ~ expansion; absolute paths must live under root.
+fn path_within_root(path: String, root: String) -> Bool {
+    if str_eq(root, "") {
+        return true
+    }
+    if str_contains(path, "..") {
+        return false
+    }
+    if str_starts_with(path, "~") {
+        return false
+    }
+    if str_starts_with(path, "/") {
+        return str_starts_with(path, root)
+    }
+    return true
+}
+
+// Resolve a relative tool path against the root so it lands inside the subtree.
+fn resolve_in_root(path: String, root: String) -> String {
+    if str_eq(root, "") {
+        return path
+    }
+    if str_starts_with(path, "/") {
+        return path
+    }
+    return root + "/" + path
+}
+
 fn dispatch_tool(tool_name: String, tool_input: String) -> String {
     if str_eq(tool_name, "read_file") {
         let path: String = json_get(tool_input, "path")
-        let content: String = fs_read(path)
+        let root: String = agent_workspace_root()
+        if !path_within_root(path, root) {
+            return json_safe("denied: path is outside the agent workspace root")
+        }
+        let content: String = fs_read(resolve_in_root(path, root))
         return json_safe(content)
     }
     if str_eq(tool_name, "write_file") {
         let path: String = json_get(tool_input, "path")
         let content: String = json_get(tool_input, "content")
-        fs_write(path, content)
+        let root: String = agent_workspace_root()
+        if !path_within_root(path, root) {
+            return json_safe("denied: path is outside the agent workspace root")
+        }
+        fs_write(resolve_in_root(path, root), content)
         return json_safe("{\"ok\":true}")
     }
     if str_eq(tool_name, "web_get") {
@@ -401,7 +463,9 @@ fn dispatch_tool(tool_name: String, tool_input: String) -> String {
     }
     if str_eq(tool_name, "run_command") {
         let cmd: String = json_get(tool_input, "command")
-        let result: String = exec_capture(cmd)
+        let root: String = agent_workspace_root()
+        let scoped: String = if str_eq(root, "") { cmd } else { "cd " + root + " && ( " + cmd + " )" }
+        let result: String = exec_capture(scoped)
         return json_safe(result)
     }
     // MCP connector tools (namespaced mcp__<server>__<tool>) are routed through
@@ -421,13 +485,21 @@ fn dispatch_tool(tool_name: String, tool_input: String) -> String {
     }
     if str_eq(tool_name, "list_files") {
         let path: String = json_get(tool_input, "path")
-        let result: String = exec_capture("ls -la " + path + " 2>&1")
+        let root: String = agent_workspace_root()
+        if !path_within_root(path, root) {
+            return json_safe("denied: path is outside the agent workspace root")
+        }
+        let result: String = exec_capture("ls -la " + resolve_in_root(path, root) + " 2>&1")
         return json_safe(result)
     }
     if str_eq(tool_name, "grep") {
         let pattern: String = json_get(tool_input, "pattern")
         let path: String = json_get(tool_input, "path")
-        let result: String = exec_capture("grep -rn \"" + pattern + "\" " + path + " 2>&1 | head -50")
+        let root: String = agent_workspace_root()
+        if !path_within_root(path, root) {
+            return json_safe("denied: path is outside the agent workspace root")
+        }
+        let result: String = exec_capture("grep -rn \"" + pattern + "\" " + resolve_in_root(path, root) + " 2>&1 | head -50")
         return json_safe(result)
     }
     if str_eq(tool_name, "edit_file") {