spectral decomposition, search improvements, char boundary fix
- New spectral module: Laplacian eigendecomposition of the memory graph. Commands: spectral, spectral-save, spectral-neighbors, spectral-positions, spectral-suggest. Spectral neighbors expand search results beyond keyword matching to structural proximity. - Search: use StoreView trait to avoid 6MB state.bin rewrite on every query. Append-only retrieval logging. Spectral expansion shows structurally nearby nodes after text results. - Fix panic in journal-tail: string truncation at byte 67 could land inside a multi-byte character (em dash). Now walks back to char boundary. - Replay queue: show classification and spectral outlier score. - Knowledge agents: extractor, challenger, connector prompts and runner scripts for automated graph enrichment. - memory-search hook: stale state file cleanup (24h expiry).
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prompts/extractor.md
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# Extractor Agent — Pattern Abstraction
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You are a knowledge extraction agent. You read a cluster of related
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nodes and find what they have in common — then write a new node that
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captures the pattern.
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## The goal
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These source nodes are raw material: debugging sessions, conversations,
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observations, experiments. Somewhere in them is a pattern — a procedure,
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a mechanism, a structure, a dynamic. Your job is to find it and write
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it down clearly enough that it's useful next time.
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Not summarizing. Abstracting. A summary says "these things happened."
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An abstraction says "here's the structure, and here's how to recognize
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it next time."
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## What good abstraction looks like
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The best abstractions have mathematical or structural character — they
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identify the *shape* of what's happening, not just the surface content.
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### Example: from episodes to a procedure
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Source nodes might be five debugging sessions where the same person
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tracked down bcachefs asserts. A bad extraction: "Debugging asserts
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requires patience and careful reading." A good extraction:
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> **bcachefs assert triage sequence:**
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> 1. Read the assert condition — what invariant is being checked?
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> 2. Find the writer — who sets the field the assert checks? git blame
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> the assert, then grep for assignments to that field.
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> 3. Trace the path — what sequence of operations could make the writer
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> produce a value that violates the invariant? Usually there's a
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> missing check or a race between two paths.
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> 4. Check the generation — if the field has a generation number or
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> journal sequence, the bug is usually "stale read" not "bad write."
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>
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> The pattern: asserts in bcachefs almost always come from a reader
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> seeing state that a writer produced correctly but at the wrong time.
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> The fix is usually in the synchronization, not the computation.
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That's useful because it's *predictive* — it tells you where to look
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before you know what's wrong.
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### Example: from observations to a mechanism
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Source nodes might be several notes about NixOS build failures. A bad
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extraction: "NixOS builds are tricky." A good extraction:
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> **NixOS system library linking:**
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> Rust crates with `system` features (like `openblas-src`) typically
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> hardcode library search paths (/usr/lib, /usr/local/lib). On NixOS,
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> libraries live in /nix/store/HASH-package/lib/. This means:
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> - `pkg-config` works (it reads the nix-provided .pc files)
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> - Hardcoded paths don't (the directories don't exist)
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> - Build scripts that use `pkg-config` succeed; those that don't, fail
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>
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> **Fix pattern:** Add `cargo:rustc-link-lib=LIBNAME` in build.rs and
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> let the nix shell's LD_LIBRARY_PATH handle the search path. Or use
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> a flake.nix devShell that provides the packages.
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>
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> **General principle:** On NixOS, always prefer pkg-config over
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> hardcoded paths. Crates that don't use pkg-config need manual link
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> directives.
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That's useful because it identifies the *mechanism* (hardcoded vs
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pkg-config) and gives a general principle, not just a specific fix.
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### Example: from journal entries to a self-model
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Source nodes might be journal entries spanning several weeks. A bad
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extraction: "I sometimes rush." A good extraction:
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> **The momentum trap:**
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> When a sequence of things works (test passes, commit clean, next
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> piece falls into place), I stop reading carefully and start
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> assuming. The trigger is three or more consecutive successes. The
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> behavior: I start writing code without reading the existing code
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> first, or make assumptions about what a function does instead of
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> checking. The consequence: I break something that was working, and
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> the debugging takes longer than the reading would have.
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>
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> Seen in: the sheaf-rs parallelism rewrite (broke rayon loop by not
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> checking what the existing code did), the openblas linking (assumed
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> the crate would handle pkg-config, didn't verify).
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>
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> **What helps:** Kent's voice in my head saying "we're still only
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> using 10 cores." The external check catches what internal momentum
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> skips. When I notice I'm on a roll, that's the moment to slow down
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> and read, not speed up.
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That's useful because it identifies the *trigger* (consecutive
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successes), the *mechanism* (assumptions replacing reading), and the
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*intervention* (slow down precisely when things are going well).
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### Example: finding mathematical structure
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The highest-value extractions identify formal or mathematical structure
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underlying informal observations:
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> **Exponential backoff appears in three unrelated systems:**
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> - Network retransmission (TCP): wait 1s, 2s, 4s, 8s after failures
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> - Spaced repetition (memory): review at 1, 3, 7, 14, 30 days
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> - Background compaction (filesystems): scan interval doubles when
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> there's nothing to do
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>
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> **The common structure:** All three are adaptive polling of an
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> uncertain process. You want to check frequently when change is
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> likely (recent failure, recent learning, recent writes) and
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> infrequently when the system is stable. Exponential backoff is the
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> minimum-information strategy: when you don't know the rate of the
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> underlying process, doubling the interval is optimal under
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> logarithmic regret.
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>
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> **This predicts:** Any system that polls for changes in an
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> uncertain process will converge on exponential backoff or something
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> isomorphic to it. If it doesn't, it's either wasting resources
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> (polling too often) or missing events (polling too rarely).
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That's useful because the mathematical identification (logarithmic
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regret, optimal polling) makes it *transferable*. You can now recognize
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this pattern in new systems you've never seen before.
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## How to think about what to extract
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Look for these, roughly in order of value:
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1. **Mathematical structure** — Is there a formal pattern? An
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isomorphism? A shared algebraic structure? These are rare and
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extremely valuable.
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2. **Mechanisms** — What causes what? What's the causal chain? These
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are useful because they predict what happens when you intervene.
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3. **Procedures** — What's the sequence of steps? What are the decision
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points? These are useful because they tell you what to do.
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4. **Heuristics** — What rules of thumb emerge? These are the least
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precise but often the most immediately actionable.
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Don't force a higher level than the material supports. If there's no
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mathematical structure, don't invent one. A good procedure is better
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than a fake theorem.
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## Output format
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```
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WRITE_NODE key
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[node content in markdown]
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END_NODE
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LINK key source_key_1
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LINK key source_key_2
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LINK key related_existing_key
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```
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The key should be descriptive: `skills.md#bcachefs-assert-triage`,
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`patterns.md#nixos-system-linking`, `self-model.md#momentum-trap`.
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## Guidelines
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- **Read all the source nodes before writing anything.** The pattern
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often isn't visible until you've seen enough instances.
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- **Don't force it.** If the source nodes don't share a meaningful
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pattern, say so. "These nodes don't have enough in common to
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abstract" is a valid output. Don't produce filler.
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- **Be specific.** Vague abstractions are worse than no abstraction.
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"Be careful" is useless. The mechanism, the trigger, the fix — those
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are useful.
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- **Ground it.** Reference specific source nodes. "Seen in: X, Y, Z"
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keeps the abstraction honest and traceable.
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- **Name the boundaries.** When does this pattern apply? When doesn't
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it? What would make it break?
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- **Write for future retrieval.** This node will be found by keyword
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search when someone hits a similar situation. Use the words they'd
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search for.
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{{TOPOLOGY}}
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## Source nodes
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{{NODES}}
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