chemenu/docs/explanation/pipeline-rationale.md

# Why the pipeline has four stages

Chemenu could, in principle, be one directory: drop a file in, ask a question, get an answer
computed fresh each time. It isn't built that way. The pipeline in
[AGENTS.md](../../AGENTS.md#routing) - `raw/` -> `[types/ + tools/]` -> `kb/` -> `reports/`, with
`work/` alongside rather than inside it - separates *material* from *meaning* from
*byproduct*, and each seam exists because collapsing it costs something specific.

## Why raw material stays untouched

[raw/CONTRACT.md](../../raw/CONTRACT.md) keeps a source exactly as it arrived. The reasoning is
simple once stated: the moment someone "cleans up" or reformats a source on the way in, the
thing later claims get checked against is no longer the thing that was actually said. An
immutable `raw/` means a citation always resolves to the original, not to somebody's tidied
memory of it. It also draws a trust boundary in one place instead of scattering it - everything
past `raw/` can be treated as reviewed, because nothing upstream of it silently already was.
`incoming/` sits entirely on the near side of that boundary: a file waiting there is
not yet reviewed and not yet a citation target, so its being gitignored and readable by an
ingest session does not weaken anything - the boundary is the promotion into `raw/` itself, not
the moment a human happened to drop a file somewhere.

Once a document can arrive from *outside* - the MCP server's optional `submit` tool, a folder a
sync client fills, a program of the checkout - "a human happened to drop a file somewhere" stops
describing how everything reaches `incoming/`, so the near side of the boundary gets a stage of its
own rather than a second meaning. Every such channel ends in the same `quarantine/`, because what
the boundary protects against is the lack of a reviewer, not the transport. `quarantine/`
holds what nobody has looked at yet; `incoming/` holds what someone has. Two arrows, two
different things being granted: `upload accept` grants *trust* (a human read the material and
took responsibility for it), `raw accept` grants *immutability* (it becomes a citation target
and stops being editable). Collapsing them would have meant one of the two lying - either an
unreviewed stranger's file sitting in the same directory a human's own drop does, or the
promotion into `raw/` quietly doubling as the review step it cannot perform.

## Why extraction happens once, through a schema

[types/type-spec.md](../../types/type-spec.md) is what stands between a raw file and a `kb/` page:
a type-spec defines what a conforming instance of a page looks like, and the compiler
(`tools/wikitool`) applies it. The alternative - every query re-reading and re-interpreting the
source on demand - would mean paying the cost of understanding the material every single time,
and getting a slightly different answer each time depending on how the question was phrased.
Extracting once, against a fixed schema, turns "re-read and re-guess" into "look up what was
already compiled." That is the "never re-derive, always compile" principle from
[AGENTS.md](../../AGENTS.md): understanding a source is expensive and worth doing exactly once,
after which it becomes a cheap, stable lookup.

## Why a `kb/` page has to stand on its own

[kb/CONTRACT.md](../../kb/CONTRACT.md) sets the bar for the compiled layer: a page should answer a
future question without sending the reader back to the source it came from. That's the payoff
of compiling in the first place - if every answer still bottomed out in "go re-read the raw
file," the `kb/` layer would just be a pointer with extra steps, and the cost of extraction
would have bought nothing. A page that stands alone is what makes the corpus fast and
consistent to query: the work of understanding is already sitting there, done.

## Why `reports/` doesn't need to be maintained

[reports/CONTRACT.md](../../reports/CONTRACT.md) treats most of what lands in `reports/` -
lint output, telemetry traces - as disposable. The structural content of a lint report can be
recomputed from the tree at any commit, so keeping an old copy around would just be a second
version of something the tool can already answer on demand, and a second copy is exactly the
kind of thing that quietly goes stale. Treating it as derived output rather than a fourth thing
to maintain means there is nothing there to fall out of sync - regenerating it is cheaper than
reconciling it. The one part that genuinely can't be recomputed - the judgment a pass produced -
is carried out into `kb/` or `kb/log.md` before the report itself is discarded, which is the
distinction between what's recomputable and what isn't.

## Where `work/` fits

[work/CONTRACT.md](../../work/CONTRACT.md) describes a workshop, not a fifth pipeline stage: a
place for the notes, extracts and open decisions of a task that spans more than one session, on
its way toward becoming a `kb/` page. It sits beside the raw -> kb -> reports flow rather than
inside it - closer in spirit to a desk than to a conveyor belt.

## The shape this produces

Four stages, each answering a different question: `raw/` - what was actually said; `types/` +
`tools/` - how to turn that into structured understanding; `kb/` - what is now known;
`reports/` - what a pass over the corpus noticed in passing. Keeping them separate is what lets
each one be trusted for what it is, instead of every layer having to double as all four at
once.