docs: mark phase 3 complete, record the skills and caching findings

Two findings that changed the plan rather than confirming it:

  23. Skills require a tool literally named `read`. Curator's tools are all
      domain-specific, so every --skill argument was discarded in silence. The
      planned split into curator-core / video-arr / books-ingest was inert before
      it was written; the policy stays in APPEND_SYSTEM.md. memo-inbox is
      unaffected because it registers a restricted `read` override, which is why
      the earlier note generalised wrongly from it.

  24. A long-lived session is worth far more than the startup it saves: 99.97% of
      input read from cache on a continuing conversation against 0% on a new one.
      That is what makes the generated tool list necessary rather than merely
      tidy -- anything varying at the front of the prompt destroys it -- and it
      makes rotation a cost to be bounded rather than applied eagerly.

profile.toml now describes the phase-3 configuration that is actually deployed,
including that the empty `skills` list is a finding and not an oversight.
pi_rpc gains --system-prompt support and no longer guesses whether a `read` tool
will exist; extension_registers_read has to be stated.

harness-layering.md records what transfers from a widely-shared account of
building a personal coding harness on pi, and what does not. The layering frame
holds and the cache-hit figure was the useful part. Its central recommendation --
installing third-party packages -- is disqualifying for an unattended agent
holding tracker credentials, and its discipline layer (AGENTS.md) is precisely
what we block, because it is discovered from every parent directory.

docs/pi-runtime-notes.md

@@ -501,6 +501,71 @@ instructions under `--system-prompt`; they have to be in the prompt text.
 
 ---
 
+## 23. Skills need a tool literally named `read`, so a domain-only agent cannot use them
+
+Section 1 recorded that `--no-tools` disables skills. The real rule is narrower and
+worse: `formatSkillsForPrompt` runs only when a tool **named `read`** is active.
+
+```js
+const customPromptHasRead = !selectedTools || selectedTools.includes("read");
+if (customPromptHasRead && skills.length > 0) {
+    prompt += formatSkillsForPrompt(skills);
+}
+```
+
+Measured with a probe registering three tools and loading one skill:
+
+| active tools | `--system-prompt` | skills section | skill names |
+|---|---|---|---|
+| `probe_read`, `query_library`, … | yes | **true** | `[…, curator-core]` |
+| `probe_read`, `query_library`, … | no | true | `[…, curator-core]` |
+| `query_library`, `lookup_online`, `counts` | yes | **false** | `[]` |
+| `query_library`, `lookup_online`, `counts` | no | **false** | `[]` |
+
+So it is not about `--system-prompt` and not about `--no-tools`. An agent whose
+tools are all domain-specific gets **nothing** from `--skill`, silently.
+
+memo-inbox is unaffected because it registers a path-restricted `read` override.
+Curator has no `read` and no reason to invent one, so its `--skill` arguments were
+discarded and the plan's split into `curator-core` / `video-arr` / `books-ingest`
+was inert before it was written. The policy stays in `APPEND_SYSTEM.md`, which is
+unconditional.
+
+`PiLaunchConfig._read_reachable` used to assume `no_builtin_tools` implied an
+extension supplying `read`. It no longer guesses: `extension_registers_read` must
+be set explicitly, and loading skills without it logs a warning.
+
+A side benefit of not using skills: on-demand injection varies the prompt, and a
+varying prefix defeats provider prompt caching. See section 24.
+
+## 24. A long-lived session is worth far more than the process startup it saves
+
+Measured on Curator's conversation path, same question, same model:
+
+| turn | cache read / billed input |
+|---|---|
+| first turn of a new session | 0% |
+| continuing session | **99.97%** |
+
+The saving is not the ~1-2 s of process startup, it is that the whole system
+prompt and prior history are re-read from cache instead of re-charged.
+
+The practical constraints that follow:
+
+- **Nothing may vary at the front of the prompt.** The tool list is generated into
+  the system prompt once (section 22) rather than injected per turn, and
+  per-request restatements of "which adapters exist" were removed.
+- **Rotation is a cost.** Each rotation resets the cache, so rotate on explicit
+  bounds (`rotate_after_prompts`, `rotate_after_messages`) rather than eagerly.
+- **Session files must persist.** Curator keys the session id on a uuid5 of the
+  chat id, so a service restart resumes the same session and keeps the cache warm.
+- **Idle processes must still be reclaimed.** A process per chat that is never
+  stopped is 100-200 MB and several tasks; the set has to be swept on a TTL or it
+  grows until `MemoryMax` or `TasksMax` produces an unexplained failure to start a
+  new conversation.
+
+---
+
 ## Re-verification
 
 ```bash