Distill

/distill

Force a distillation pass now. The daemon's background distill cycles run on its own clock; /distill is the explicit user-triggered pass.

Mental model

Distillation is four operations bundled into one flow:

• emerge — cluster new memories into new pages
• absorb — assign orphan memories to existing pages, propose new pages from topics that 2+ existing pages link to but no page is named for
• refresh — regenerate stale pages from their source memories (only when the user has not edited the page; pages you have touched stay locked)
• merge — combine duplicate pages flagged by the daemon's global review

The default flow runs all four. The rebuild verb is a destructive opt-in that overrides the lock on a single page.

Single flow

One POST to the daemon. Response splits into:

• pages_created / created_ids: pages the daemon synthesized itself (only when daemon has an LLM).
• pending: clusters the daemon couldn't finish. The agent synthesizes each in this session and POSTs them back to /api/pages.

Trigger timing is the only thing that differs between background distill cycles and this skill. Code path is the same; daemon hands back clusters when it can't synthesize; whoever called fills in the rest.

Flow

1. Pick the scope

For bare /distill, infer a target from cwd:

Bash: top=$(git -C "$PWD" rev-parse --show-toplevel 2>/dev/null); \
      common=$(git -C "$PWD" rev-parse --git-common-dir 2>/dev/null); \
      if [ -n "$common" ]; then \
        case "$common" in /*) root=$(dirname "$common");; *) root=$(cd "$top" && cd "$(dirname "$common")" && pwd);; esac; \
        basename "$root"; \
      fi

• Output → use it (e.g. origin).
• Not a git repo → fall back to basename "$PWD".
• Reserved keyword deep → no scope (global pass).
• Reserved keyword sequence rebuild <page-id> → call distill(target=<page-id>, force=true). Confirms "Rebuild page ? Your edits will be wiped, page regenerates from sources." before proceeding. Skip the rest of this skill — single-page rebuild does not produce pending clusters; the daemon's response shape is {"status": "ok", "force": true, "page_id": ..., "updated": true}. Report verbatim.

For /distill <arg> → forward <arg> to target.

2. Call the MCP tool

distill(target="<scope>")

The tool returns the daemon's full JSON payload as text. Parse it as JSON. Possible shapes:

{
  "pages_created": 0,
  "scoped": true,
  "created_ids": [],
  "pending": [
    { "source_ids": [...], "contents": [...], "entity_id": ...,
      "entity_name": ..., "space": ..., "estimated_tokens": ... },
    ...
  ],
  "stale_pages": [
    { "page_id": ..., "title": ..., "summary": ...,
      "source_memory_ids": [...], "stale_reason": "source_updated",
      "user_edited": false, "sources_updated_count": 3 },
    ...
  ],
  "stale_truncated": false,
  "orphan_topics": [
    { "label": "Topic Z", "count": 3 },
    ...
  ]
}

The route never invokes the daemon LLM. created_ids is always empty when called from this skill; pending carries every cluster the daemon found. The agent synthesizes them in this session — that's why the LLM choice is consistent with how the user invoked the skill.

unresolved + hint: relay to user verbatim and stop.

3. Synthesize each pending cluster

The daemon route filters out clusters fully covered by an existing page (subset or Jaccard ≥ 0.8). What remains is either:

• A brand-new cluster (no existing page) → create a new page.
• A refresh candidate (existing_page_id is set) → the cluster has new memories beyond what's in the matched page. The agent has LLM access, so the right move is to refresh the existing page in the same pass.

Cluster shape:

pending: [
  {
    source_ids, contents, entity_id, entity_name, space,
    estimated_tokens,
    existing_page_id?, existing_page_title?, new_memory_count?
  },
  ...
]

For each cluster, first run a coherence check before synthesizing:

• Skim every memory in cluster.contents.
• If the cluster has ≥ ~4 memories and the topics scatter (entity shared but the memories cover unrelated sub-topics — e.g. all tagged Origin but spanning RwLock bugs, schema choices, onboarding UI, migrations, and CSS), the cluster is incoherent. Skip synthesizing it. Record it for the report under "Skipped (low coherence)" with the existing page title (if refresh) or a short topic hint (if new).
• Coherent cluster (memories share an actual topic, not just an entity tag) → proceed to synthesis.

The coherence judgement is something only the agent can do — it needs to read the prose. Daemon clustering is heuristic; agent is the final filter against producing a grab-bag page.

For each coherent cluster:

• Title: short noun phrase. Use existing_page_title when refreshing unless the new memories materially change the topic. For new clusters: cluster.entity_name if specific, otherwise derive from the first memory's content.
• Summary: one sentence — the durable claim.
• Body: 3-7 paragraphs of wiki prose. Use [[wikilinks]]. Cite source ids inline with (source: mem_XXX).

New cluster (no existing_page_id) — call the MCP tool:

create_page(title="...", summary="...", content="...",
            entity_id="<cluster.entity_id or omit>",
            space="<cluster.space>",
            source_memory_ids=[...])

Refresh candidate (existing_page_id is set) — replace the body in place via the update_page MCP tool. This is a single atomic call: replaces content + source list + optional summary, clears the daemon's stale_reason, bumps version, preserves page_id + created_at so external [[wikilinks]] keep working.

update_page(page_id=cluster.existing_page_id,
            content="...",
            source_memory_ids=cluster.source_ids,
            summary="...")

3.5 Refresh stale pages

The stale_pages block in the response lists pages whose sources changed since last compile. Shape:

stale_pages: [
  { page_id, title, summary, source_memory_ids,
    sources_updated_count, stale_reason, user_edited },
  ...
]
stale_truncated: <bool>   # true when 10+ stale pages exist

For each stale page:

• user_edited == true → never auto-rewrite. The user touched the page; the upstream memories also changed. Surface in the "Conflict" report block and stop. The user resolves by hand, OR runs /distill rebuild <page-id> to wipe their edits and regenerate from sources.
• user_edited == false → fetch source memories via get_page_sources(page_id="<id>"), run the same coherence check used for clusters, then call update_page with the existing source_memory_ids and freshly synthesized prose.

update_page(page_id=stale.page_id,
            content="<refreshed prose>",
            source_memory_ids=stale.source_memory_ids,
            summary="<optional refreshed claim>")

When stale_truncated == true, tell the user "more stale pages remain — re-run /distill after this pass to continue."

3.6 Surface orphan-topic suggestions

orphan_topics lists wikilink labels that 2+ existing pages reach for but no page is named for. Each entry is a topic-discovery signal — other pages are asking for this page.

Do not auto-create pages from this list — the agent doesn't have the source memories at hand, and an empty-stub page is worse than no page. Surface them in the report so the user can choose to run /distill <label> intentionally:

Topic suggestions (other pages link here, no page yet):
  - "Topic Z"  (3 pages reference it)
  - "Other"    (2 pages reference it)

Skip the section when orphan_topics is empty.

4. Report terse

Three output shapes. Pick the one that matches what happened.

If pending is empty (every cluster already fully covered):

Scope `<scope>` is up to date — no new memories to distill.

If at least one cluster was synthesized:

Distilled N page(s) from <total> memories in scope `<scope>`:
  - <Title>  v1, synthesized from <K> sources
  - <Title>  v3 → v4: +mem_xyz, +250 chars
  ...

For each page, create_page and update_page return a WriteResult whose warnings array carries a pre-formatted delta line from the daemon (e.g. "v3 → v4: +mem_xyz, +250 chars"). Render it verbatim after the title. When warnings is empty or the call returned no WriteResult, fall back to:

• New page: v1, synthesized from <K> sources (K = source_ids length)
• Refreshed page: refreshed (bare, as before)

This lets the user see exactly what changed per page without opening each file.

If at least one cluster was skipped on the coherence check:

Skipped M cluster(s) — low coherence (memories share entity but
topics scatter; would produce a grab-bag page):
  - "<existing_page_title or topic hint>"  (<N> memories)
  ...

If at least one stale page was refreshed:

Refreshed K stale page(s):
  - <Title>  v2 → v3: +mem_abc, +180 chars
  - <Title>  refreshed
  ...

Same delta-line rule as new/refresh clusters: render warnings[0] from the update_page WriteResult verbatim; fall back to refreshed when absent.

If at least one stale page was skipped because user_edited:

Conflict on L stale page(s) — page has user edits, sources also
changed. Open and reconcile manually:
  - <Title>  (~/.origin/pages/<slug>.md)

Distinct wording from the coherence-skip block so the user can tell the two reasons apart at a glance.

Emit the blocks back-to-back when more than one outcome happened in the same pass.

When the only outcome is skipped clusters (and pending was non-empty), still emit the Skipped block. Do not report "up to date" in that case — the scope isn't up to date, the candidates were just too low quality.

Rules:

• Titles, not page ids. Ids visually truncate; titles read clean.
• One line per synthesized page. No body in chat — /read "<title>" for that.
• <total> = sum of source_ids.len() across the clusters that were actually synthesized.
• If the pass produced fewer pages than expected, it's the clustering thresholds. Most memories sit alone without enough peers to form a cluster of 3+. Capture more on the same topic to grow them.

Auto-commit ~/.origin/

After writing the pages above, snapshot the change so the user can git log their memory's life timeline. Defensive — silent skip if git is missing or ~/.origin/ is not a repo yet.

Bash: git -C ~/.origin add -A && \
      git -C ~/.origin -c user.name=Origin -c user.email=daemon@origin.local \
          commit --quiet -m "distill: <N> pages" 2>/dev/null || \
      (sleep 1 && git -C ~/.origin add -A && \
       git -C ~/.origin -c user.name=Origin -c user.email=daemon@origin.local \
           commit --quiet -m "distill: <N> pages" 2>/dev/null) || true

The retry handles index.lock races — the daemon may be writing to ~/.origin/ at the same moment (auto-commit from captures). One-second wait is enough for the daemon to release the lock.

When to use

• User says "distill", "synthesize", "rebuild the page on X".
• After a bulk import — daemon distill cycles handle this in the background; user can force a pass for immediate visibility.
• /distill rebuild <page-id> when you want to wipe a page you previously edited and have the daemon regenerate from current sources. Destructive: your prose goes away. Use after you are done curating a page and want it back on the auto-refresh path.

When NOT to use

• Trivial / one-off interactions. The background scheduler covers periodic refresh.
• Single memory write → daemon's post-ingest enrichment already covers it.

Cost

Each cluster the agent synthesizes counts against this session's tokens. Daemon-side clusters (when an LLM is present) cost daemon LLM tokens instead (cents on API, seconds on-device). Either way, keep cluster sizes reasonable — the daemon already enforces a per-cluster token budget via its tuning config.