pi-agent-config/docs/pi-runtime-notes.md

# Pi Runtime Notes

> Verified against **pi 0.84.3** on Debian 13 / node v22.23.2, 2026-08-27.
> Every claim below is either quoted from `dist/` source or reproduced by the
> probe harness in [`evidence/probe-harness/`](evidence/probe-harness/).
> Results: [`evidence/2026-08-27-isolation-probe.md`](evidence/2026-08-27-isolation-probe.md).

This file records behaviour that the official docs either do not state or state
only in passing, but which determines whether a dedicated Pi agent works at all.
Re-verify after every `pi update`.

---

## 1. The skills section requires an active `read` tool

`dist/core/system-prompt.js`:

```javascript
const hasRead = tools.includes("read");
// Append skills section (only if read tool is available)
if (hasRead && skills.length > 0) {
    prompt += formatSkillsForPrompt(skills);
}
```

`tools` is the **active** tool-name list, passed as `selectedTools` from
`agent-session.js:_rebuildSystemPrompt(this.getActiveToolNames())`.

**Consequence:** `--no-tools` silently removes the entire skills block.
Any `SKILL.md` is then unreachable, and `--skill <path>` becomes a no-op.

Probe evidence (`--no-tools` vs `--no-builtin-tools`):

| Flags | `available_skills` in prompt | prompt length |
|---|---|---|
| `--no-tools` | **false** | 1859 |
| `--no-builtin-tools` | true | 3413 |

This was a live defect in the Curator scenario: it ran `--no-tools --skill …`
for its whole lifetime, so its 64-line media policy never reached the model.

## 2. Skill injection is progressive, not full text

`formatSkillsForPrompt` emits only `<name>`, `<description>` and `<location>`
per skill, plus the instruction "Use the read tool to load a skill's file when
the task matches its description."

So the body of a `SKILL.md` costs nothing up front but **is only ever read via
the `read` tool**. A skill body is unreachable without a working `read`.

Corollary: if you override `read` with a path-restricted implementation, the
allowlist must include the skill directory or skill bodies cannot be loaded.

## 3. `--skill` does not double-load an auto-discovered skill

`dist/core/skills.js:loadSkills()` dedupes twice — by canonical realpath, and
by skill `name`. Defaults are added first, so on a name collision the
**auto-discovered** skill wins and a collision diagnostic is emitted.
Same file via symlink is skipped silently.

## 4. Tool gating semantics

| Flag | registry filter | initial active set | extension tools |
|---|---|---|---|
| *(none)* | none | `settings.defaultTools ?? [read,bash,edit,write]` | all activated |
| `--tools a,b` | **strict allowlist across every source** | `[a,b]` | must be named to exist |
| `--no-tools` | empty allowlist | `[]` | **also killed** |
| `--no-builtin-tools` | none | `[]` | **all activated** |
| `--exclude-tools x` | removes `x` | filtered | applies to all sources |

From `dist/core/agent-session.js`:

```javascript
const isAllowedTool = (name) =>
  (!allowedToolNames || allowedToolNames.has(name)) && !excludedToolNames?.has(name);
```

Under `--no-builtin-tools` the built-ins stay **registered but inactive**, so an
extension can re-enable them with `pi.setActiveTools([...])`. Under `--no-tools`
they were never registered and cannot be revived.

Probed: `--no-builtin-tools` + one extension →
`ACTIVE_TOOLS=["probe_plain_schema","read"]`, while `bash/edit/write/grep/find/ls`
remain listed as `[builtin]` and inactive.

## 5. `registerTool` accepts a plain JSON Schema object — verified

Declared type is TypeBox `TSchema`, but a raw JSON Schema object works:

```typescript
pi.registerTool({
  name: "probe_plain_schema",
  parameters: { type: "object", properties: { q: { type: "string" } }, required: ["q"] } as any,
  ...
});
```

Probe result: the tool appears as `probe_plain_schema[cli]` and is active.

**Why this matters:** a backend can serve its tool definitions as JSON Schema
over HTTP and a generic bridge extension can register them at runtime, so the
schema has exactly one source of truth. See `shared/extensions/`.

Note `--tools` is a *registry-level* allowlist, so dynamically registered tools
must either be named in `--tools` or you must use `--no-builtin-tools`
(no allowlist) and let the extension govern the active set.

## 6. An extension can override a built-in tool by name — verified

Registering `name: "read"` replaces the built-in in the registry: the probe
showed `read[cli]` instead of `read[builtin]` while other built-ins kept
`[builtin]`. This is the supported way to give an agent a path-restricted
`read` while still satisfying the requirement in §1.

`memo-guard.ts` in the memo-inbox scenario has used this in production.

## 7. Only tools with `promptSnippet` appear in the human-readable tool list

`dist/core/system-prompt.js`: "A tool appears in Available tools only when the
caller provides a one-line snippet."

The tool *schemas* are always sent through the provider's tool-calling API, so
an omitted `promptSnippet` does not break invocation — but the model loses the
prose overview. Always set `promptSnippet`, and `promptGuidelines` where useful.

## 8. `.pi/SYSTEM.md` replaces the default prompt; the replacement branch omits tools and guidelines

Default prompt (`system-prompt.js:82`) begins:

> You are an expert coding assistant operating inside pi, a coding agent harness.
> You help users by reading files, executing commands, editing code, and writing new files.

and ends with a block of **absolute paths to pi's own README / docs / examples**
plus "read the docs and examples, and follow .md cross-references before
implementing".

For a non-coding agent this is not merely noise: it is a ready-made escalation
path for prompt injection.

The `customPrompt` branch (`system-prompt.js:13-33`) concatenates only:

```
SYSTEM.md → APPEND_SYSTEM.md → <project_context>(AGENTS.md) → skills section → cwd
```

It does **not** include `toolsList` or `Guidelines`. A replacement `SYSTEM.md`
must therefore carry its own tool overview and output discipline.

`.pi/SYSTEM.md` lives under `.pi/`, so it requires **project trust** — pass
`--approve` in non-interactive modes.

Probe evidence:

| Combination | coding-assistant text | pi-docs block | SYSTEM.md applied | prompt length |
|---|---|---|---|---|
| isolation flags only | true | true | false | 2619 |
| `+ .pi/SYSTEM.md + --approve` | **false** | **false** | **true** | **960** |

## 9. Context files are loaded from every parent directory, and `AGENTS.override.md` does not stop that

Load order: `~/.pi/agent/AGENTS.md`, then each parent directory walking up from
cwd, then cwd.

`AGENTS.override.md` replaces `AGENTS.md`/`CLAUDE.md` **for its own directory
only**. Parent directories still layer normally — the docs say so explicitly
("Context files from other directories still layer normally") and it is easy to
get this wrong.

Probed: with `AGENTS.override.md` present in the workspace and a marker file at
`/tmp/AGENTS.md`, the marker **still appeared** in the system prompt.

| Configuration | parent `/tmp/AGENTS.md` in prompt |
|---|---|
| workspace has `AGENTS.override.md` | **yes** |
| `--no-context-files` (`-nc`) | no |

So a stray `~/AGENTS.md` or `~/pi-workspaces/AGENTS.md` silently contaminates
every scenario rooted below it, and an override file will not save you. Neither
existed on this host as of 2026-08-27, but nothing prevents one from appearing.

**The only way to make the personality deterministic is `-nc`.** Since that also
drops the workspace's own context file, the durable role content has to move into
`.pi/SYSTEM.md` and `.pi/APPEND_SYSTEM.md`, which are system-prompt files rather
than context files and are therefore unaffected by `-nc`.

Verified combination — no coding-assistant framing, no pi-docs block, own
identity and role text present, parent pollution absent, only the scenario's own
skill listed:

```
--no-builtin-tools --no-extensions -e <ext> --no-skills --skill <dir>
--no-prompt-templates --no-themes --approve -nc
+ .pi/SYSTEM.md + .pi/APPEND_SYSTEM.md
```

Note also that `cwd` is what anchors this discovery: launching pi from the wrong
working directory silently drops `.pi/SYSTEM.md` and every workspace context
file. A probe that forgot `cwd` produced a 2601-character prompt with the
coding-assistant persona intact; with the correct `cwd` it produced 4082
characters with the persona replaced.

## 10. Project trust gates `.pi/`, and CLI `-e` bypasses it

Trust is required when the directory contains `.pi/settings.json`,
`.pi/{extensions,skills,prompts,themes}`, `.pi/SYSTEM.md`,
`.pi/APPEND_SYSTEM.md`, or a project `.agents/skills`. A bare `.pi` does not
count.

Always loaded regardless of trust: `AGENTS.override.md`, `AGENTS.md`,
`CLAUDE.md`, user/global extensions, and **CLI `-e` extensions** — the last one
is deliberate so they can handle the `project_trust` event.

Non-interactive modes (`-p`, `--mode json`, `--mode rpc`) never prompt; they use
`defaultProjectTrust` (`ask` default / `always` / `never`) unless `--approve` /
`--no-approve` overrides for the run.

**Design consequence:** loading a scenario extension with an absolute
`-e /path/to/ext.ts` avoids the trust question entirely, which is the most
robust option for a systemd-managed gateway.

## 10b. `PI_CODING_AGENT_DIR` isolates the agent directory — but not `~/.agents/skills`

```
PI_CODING_AGENT_DIR   Override the config directory; default is ~/.pi/agent
```

This is the strongest isolation lever available, and it is stronger than the
`--no-*` flags because it repoints **credentials and trust** as well as
resources. The `pi-grok` scenario on this host uses it:

```sh
export PI_CODING_AGENT_DIR="$PI_GROK_HOME/.pi-agent"
```

Measured, with a marker extension planted in both directories and no `--no-*`
flags at all:

| Resource | default agent dir | `PI_CODING_AGENT_DIR=<iso>` |
|---|---|---|
| `<dir>/extensions/*` | `DEFAULT_EXT_LOADED` | `ISO_EXT_LOADED` — **isolated** |
| `<dir>/skills/*` | *(none)* | `iso-skill` present — **isolated** |
| `~/.agents/skills/*` | `find-skills, modsearch, summarize` | `find-skills, modsearch, summarize` — **still leaks** |

So it isolates `settings.json`, `models.json`, `auth.json`, `trust.json`,
`extensions/`, `skills/`, `prompts/` and `themes/` **under the agent directory**,
but `~/.agents/skills/` is a separate discovery root that it does not touch.

Practical consequences:

* Use `PI_CODING_AGENT_DIR` per scenario when scenarios should not share
  provider credentials, trust decisions or model defaults. It is the only way to
  stop one scenario's `auth.json` from being readable by another's agent.
* It does **not** replace `--no-skills`. Keep the loading flags as well.
* A companion variable exists: `PI_CODING_AGENT_SESSION_DIR`, overridden by
  `--session-dir`.

## 10c. `--append-system-prompt` accepts a file path

The help text says "Append text **or file contents**". `pi-grok` relies on this:

```sh
--append-system-prompt "$PI_GROK_HOME/AGENTS.md"
```

This is a third way to inject durable role text, alongside
`.pi/APPEND_SYSTEM.md` and `AGENTS.md`. Unlike a context file it is immune to the
parent-directory walk, and unlike `.pi/APPEND_SYSTEM.md` it needs no project
trust. Useful when the role text must live outside the workspace.

## 11. User-global resources leak into every scenario

Probed with no isolation flags, from an unrelated workspace, the skills list was:

```
PROBE_SKILLNAMES=["find-skills","modsearch","summarize"]
```

Those come from `~/.agents/skills/`. `find-skills` in particular instructs the
agent to discover and install further skills — an unwanted capability surface
for a narrow-purpose agent. `~/.pi/agent/extensions/*.ts` leak the same way.

With `--no-skills --skill <abs>` the list becomes exactly `["probe-skill"]`.

## 12. No output-schema flag; use a terminating tool with constrained sampling

There is no `--output-schema` / `--response-format`. Structured output is
achieved with a tool whose `parameters` is the desired schema:

```typescript
{
  name: "emit_result",
  parameters: <schema>,
  constrainedSampling: { type: "json_schema", strict: "prefer" },
  async execute(_id, params) {
    return { content: [...], details: params, terminate: true };
  }
}
```

`ConstrainedSamplingConfig`:

```typescript
| { type: "json_schema"; strict: "prefer" | "require" }
| { type: "grammar"; variants: Partial<Record<"openai_lark" | "openai_regex", string>> }
```

`strict: "prefer"` falls back gracefully; `"require"` fails the request if the
provider cannot honour it. `terminate: true` ends the turn only when *every*
finalized tool result in the batch sets it.

This replaces regex-scraping JSON out of prose.

## 13. Tools must truncate their own output

Built-in caps are **50 KB** and **2000 lines**. Helpers exported for this:
`truncateHead`, `truncateTail`, `truncateLine`, `formatSize`,
`DEFAULT_MAX_BYTES`, `DEFAULT_MAX_LINES`.

Errors: **throw** from `execute` to set `isError: true`. Returning an
error-shaped object does not mark the call failed.

`AgentToolResult.content` goes to the model; `details` is persisted in the
session but **not** sent to the model.

## 14. Per-call gating hook

```typescript
pi.on("tool_call", async (event) => {
  if (!ALLOWED.includes(event.toolName)) {
    return { block: true, reason: "…" };
  }
});
```

`ToolCallEventResult = { block?, reason?, terminate? }`. To rewrite arguments,
mutate `event.input` in place. Later handlers observe earlier mutations and no
re-validation happens afterwards.

Combined with `pi.setActiveTools()` on `session_start` and
`resources_discover`, this gives two independent layers of capability control
that survive a mistake in the CLI flags.

## 15. RPC mode is strict JSONL and is meant to be long-lived

`--mode rpc`: commands as JSON objects on stdin, one per line; responses and
events as JSON lines on stdout.

> Split records on `\n` only. Accept optional `\r\n` by stripping a trailing
> `\r`. Node `readline` is **not** protocol-compliant because it also splits on
> `U+2028`/`U+2029`, which are valid inside JSON strings.

33 commands, including `prompt`, `steer`, `follow_up`, `abort`, `new_session`,
`get_state`, `set_model`, `set_thinking_level`, `compact`,
`set_auto_compaction`, `get_session_stats`, `switch_session`, `fork`,
`get_entries`.

`message_update` carries **deltas only** — no cumulative `message`, no
`partial`. Treat `message_end.message` as authoritative.

There is **no** command to inject a tool result from the host. Host-side
capabilities must be exposed as an extension tool that calls back out.

Probing `get_state` alone starts the agent, fires `session_start`, and exits
without ever contacting the model — a zero-cost way to inspect the resolved
system prompt and tool set.

## 16. Usage and cost are recorded per assistant message

Every `AssistantMessage` carries:

```typescript
Usage { input, output, cacheRead, cacheWrite, totalTokens,
        cost: { input, output, cacheRead, cacheWrite, total } }
```

`ToolResultMessage`, `CompactionEntry` and `BranchSummaryEntry` carry an
optional `usage` for nested LLM work. Live equivalent: RPC
`get_session_stats`, which also returns
`contextUsage { tokens, contextWindow, percent }`.

Observability therefore needs no extra instrumentation — read the session JSONL
or subscribe to `message_update`.

## 17. Sessions never rotate or expire

`--session-id <id>` is an idempotent "use this project session, create if
missing" primitive (mutually exclusive with `--session`, `--continue`,
`--resume`; validated against `^[A-Za-z0-9](?:[A-Za-z0-9._-]*[A-Za-z0-9])?$`).

There is no built-in TTL, rotation, size cap or pruning. Files grow
monotonically until deleted by hand.

## 18. Auto-compaction rarely triggers on large-context models

Condition: `contextTokens > contextWindow - reserveTokens`.

```json
{ "compaction": { "enabled": true, "reserveTokens": 16384, "keepRecentTokens": 20000 } }
```

With a 1,050,000-token context window the threshold is ~1.03 M tokens, so
latency and cost degrade for a very long time before compaction ever fires.
A gateway must implement its own rotation policy — see
[`gateway-patterns.md`](gateway-patterns.md).

## 19. `allowed-tools` in SKILL.md frontmatter is not enforced

`dist/core/skills.js:loadSkillFromFile` consumes only `name`, `description` and
`disable-model-invocation`. `allowed-tools` is documented as experimental and is
**not read** in 0.84.3.

The memo-inbox scenario declares `allowed-tools:` in its `SKILL.md`; the real
enforcement is the `ALLOWED_TOOLS` array plus `setActiveTools` and the
`tool_call` hook inside `memo-guard.ts`. Do not rely on the frontmatter field
for security.

## 20. There is no sandbox

`docs/security.md`: "Pi does not include a built-in sandbox. Built-in tools can
read files, write files, edit files, and run shell commands with the permissions
of the pi process. Extensions are TypeScript modules that run with the same
permissions."

A path-restricted `read` override is an application-level boundary, not a kernel
one. Real isolation requires bubblewrap / container / micro-VM; pi ships
`examples/extensions/sandbox/` (bubblewrap, `.pi/sandbox.json`) and
`examples/extensions/gondolin/` (micro-VM) as starting points.

---

## 21. An extension that fails to import is silent, and the agent then invents facts

Two failure modes, only one of which is reported:

| condition | exit | stderr |
|---|---|---|
| `--extension` path does not exist | 1 | `Failed to load extension ...` plus a hint |
| extension exists but throws while importing | **0** | **empty** |

The second registers no tools and says nothing. Measured with an extension whose
only defect was importing `ExtensionAPI` from `@getpi/pi` instead of
`@earendil-works/pi-coding-agent`.

What the agent did with no tools, asked which versions of a series were in the
library:

```
《权力的游戏》（Game of Thrones）1 个版本：
- 4K 实例，已跟踪
- 8 季，共 73 集，文件已齐（73/73）
- 画质：2160p WEB-DL
- 占用空间：624.7 GB
```

Every line is fabricated, and the size happens to be close to the real figure.
A later run of the same prompt said it had no data at all. So the failure is not
only silent but inconsistent: sometimes a refusal, sometimes a confident and
detailed invention.

**Therefore**: do not treat process exit status as evidence that the tools
loaded. Curator detects activation at the bridge, which the extension must call
to obtain its tool list, and refuses to proceed without it
(`curator/agent_api.py`, `wait_for_activation`).

## 22. `--system-prompt` suppresses the tool list, so `promptSnippet` is inert

`dist/core/system-prompt.js` builds `toolsList` from `promptSnippet` and
`guidelines` from `promptGuidelines` — but the `customPrompt` branch returns
before either is assembled:

```js
if (customPrompt) {
    let prompt = customPrompt;
    if (appendSection) prompt += appendSection;
    // context files, then skills (only when a `read` tool is active)
    prompt += `\nCurrent working directory: ${promptCwd}\n`;
    return prompt;              // toolsList and guidelines never appear
}
```

The tools remain callable: their schemas still go to the provider as tool
definitions. The model simply is not told in prose that it has them.

Measured effect on the same question, four runs, extension loading correctly:

| runs | behaviour |
|---|---|
| 1 | called `query_library`, answered from the result |
| 3 | called nothing, answered "I was not given any library results" |

After writing the tool list into the system prompt itself, four different
prompts each used the right tools and none answered unaided.

**Therefore**: an agent using `--system-prompt` must enumerate its own tools in
that prompt. Curator generates the section from the same specs the bridge serves
(`contracts.render_tool_prose`) and `scripts/verify-generated.sh` fails the
commit when the two drift.

This also means `promptGuidelines` cannot be relied on for safety-relevant
instructions under `--system-prompt`; they have to be in the prompt text.

---

## Re-verification

```bash
cd docs/evidence/probe-harness
./collect-evidence.sh > ../$(date -u +%Y-%m-%d)-isolation-probe.md
```

The harness costs zero model tokens: it sends a single `get_state` over RPC and
reads the resolved system prompt from `session_start`.