docs: added environment variable documentation for script nodes

Graph-Agents.md

@@ -70,6 +70,10 @@ mcp_servers:                         # MCP servers available to nodes
   - pubmed-search
 conversation_starters:               # suggested prompts in the UI
   - "Research WebAssembly outside of the browser"
+variables:                           # optional; agent variables
+  - name: project_dir                # exposed to script nodes as
+    description: Project root        # LLM_AGENT_VAR_PROJECT_DIR, overridable
+    default: "."                     # via `--agent-variable` at runtime
 
 settings:
   max_loop_iterations: 100     # PER-NODE visit cap; default 100 (see below)
@@ -96,13 +100,21 @@ nodes:
   else fails at startup. This is the *graph schema* version, not your
   agent's version.
 - **Agent-level config** (`model`, `temperature`, `top_p`, `global_tools`,
-  `mcp_servers`, `conversation_starters`) are all optional.
+  `mcp_servers`, `conversation_starters`, `variables`) are all optional.
   These are the same fields a normal agent's `config.yaml` carries; in a
   graph agent they live at the top of `graph.yaml` instead. `model` /
   `temperature` / `top_p` act as the defaults for `llm` nodes that don't
   set their own. `global_tools` and `mcp_servers` define the tool universe
   that an `llm` node's `tools:` whitelist selects from (a node with no
 `tools:` field gets none of them).
+- **`variables`:** Same shape as a normal agent's `variables:` block.
+  Each declared variable becomes available to script nodes as the env var
+  `LLM_AGENT_VAR_<UPPER_NAME>`, exactly like bash tools called by normal
+  agents. Values may be overridden at runtime via
+  `loki -a <agent> --agent-variable <name> <value> "..."`. For LLM nodes to
+  see a variable inside prompts, seed its value into state (typically via
+  a setup script that reads the env var and writes it into state) so
+  `{{name}}` resolves.
 - **`can_spawn_agents` is derived, not declared.** A graph agent can spawn
   child agents iff its graph contains at least one `agent` node. You don't
   set a flag. The `agent` node's presence *is* the declaration.
@@ -233,15 +245,37 @@ route_after_parse:
     last_run: "{{some_value}}"
 ```
 
-The script receives the current state in two forms; use whichever fits:
+### Environment
+
+The script receives the current graph state in one of two forms (use whichever fits):
 
 | Env var            | Contents                                                      |
 |--------------------|---------------------------------------------------------------|
 | `GRAPH_STATE`      | Inline JSON when serialized state is <= 32 KiB                |
 | `GRAPH_STATE_FILE` | Path to a temp JSON file when serialized state exceeds 32 KiB |
 
-Exactly one of the two is set per script invocation; **always check both**. The temp
-file (when used) is cleaned up automatically after the graph finishes.
+Exactly one of the two is set per script invocation; **always check both**.
+The temp file (when used) is cleaned up automatically after the graph finishes.
+
+Script nodes also receive the same environment that custom agent tools get when called
+from normal agents:
+
+| Env var                  | Contents                                                       |
+|--------------------------|----------------------------------------------------------------|
+| `LLM_ROOT_DIR`           | Loki config dir (e.g. `~/.config/loki`)                        |
+| `LLM_PROMPT_UTILS_FILE`  | Absolute path to `.shared/prompt-utils.sh`                     |
+| `LLM_AGENT_DATA_DIR`     | The agent's own data directory (where this `graph.yaml` lives) |
+| `LLM_AGENT_VAR_<NAME>`   | One per declared `variables:` entry; uppercased name           |
+| `PATH`                   | Loki's functions bin dir prepended to the inherited `PATH`     |
+| `CLICOLOR_FORCE`, `FORCE_COLOR` | Both set to `1` so child tools emit ANSI colors         |
+
+The script's **working directory** is the loki invocation directory (where
+the user ran `loki -a <agent> ...`), not the agent directory. This matches
+the behavior of bash tools called by normal agents, and lets scripts use
+`"."` or relative paths to refer to the user's project. To resolve sibling
+files inside the agent directory (for example `.shared/utils.sh`), use
+`"$(dirname "$0")"` from inside the script. Note that`$0` is an absolute path to
+the script file itself.
 
 The script must print a single JSON object on stdout. All keys merge into
 state; the reserved `_next` key is extracted and overrides the default `next`