intake: several configured intake channels (mcp, folder, command) all end in quarantine/ (was mcp-upload/), and upload collect pulls the synced-folder and command channels into it (#213); 10.0.0-beta.11

Files changed:
- .gitignore
- CHANGES.md
- VERSION
- docs/explanation/architecture.md
- docs/explanation/pipeline-rationale.md
- docs/how-to/README.md
- docs/how-to/back-up-to-a-synced-folder.md
- docs/how-to/collect-from-a-synced-folder.md
- docs/how-to/ingest-a-source.md
- docs/how-to/set-up-the-mcp-server.md
- docs/reference/commands/README.md
- docs/reference/commands/git.md
- docs/reference/commands/instance-health.md
- docs/reference/commands/raw-material-and-uploads.md
- docs/reference/configuration.md
- instructions/gates.md
- instructions/ingest-queue.md
- instructions/mcp-read-server.md
- instructions/migrations/10.0.0-settings-tiers.md
- instructions/wiki-ingest/SKILL.md
- raw/CONTRACT.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/cli_contract.py
- tools/chemenu/collect.py
- tools/chemenu/commands/backup_cmd.py
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/commands/doctor.py
- tools/chemenu/commands/raw/pending.py
- tools/chemenu/commands/upload_cmd.py
- tools/chemenu/config.py
- tools/chemenu/config_shapes.py
- tools/chemenu/legacy_settings.py
- tools/chemenu/mcp/server.py
- tools/chemenu/reference_doc.py
- tools/chemenu/tests/test_backup.py
- tools/chemenu/tests/test_collect.py
- tools/chemenu/tests/test_config_shapes.py
- tools/chemenu/tests/test_doctor.py
- tools/chemenu/tests/test_legacy_settings.py
- tools/chemenu/tests/test_mcp_server.py
- tools/chemenu/tests/test_upload.py
- tools/chemenu/tests/test_upload_cmd.py
- tools/chemenu/upload.py

Co-Authored-By: Claude Code <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2

instructions/ingest-queue.md

@@ -1,18 +1,19 @@
 ---
 type: types/instruction.md
 name: ingest-queue
-description: Review a document submitted from outside through the MCP submit tool before it is promoted into incoming/ - what to check, how the quarantine and its ledger work, and the Upload Review Gate that stands between a submission and raw/
+description: Review a document that reached the quarantine from outside - through the MCP submit tool, a synced folder or a command of this checkout - before it is promoted into incoming/ - what to check, how the quarantine and its ledger work, and the Upload Review Gate that stands between a submission and raw/
 ---
 
 # Reviewing an external submission
 
-An `upload` section in `.wikitool-local.json` opts a checkout into a sixth MCP tool, `submit` -
-documents pushed by a caller that is not this terminal, into a quarantine no
-ordinary command reads. This is the human half of that path: what a reviewer
-checks before letting one through, and how `upload accept`/`upload reject`
-work. What the tool itself enforces (identity, size, extension, quota,
-duplicate-hash) is `chemenu/upload.py`'s job and is not repeated here - read
-this when a submission is already waiting and a decision is due.
+The `intake` section in `.wikitool-local.json` opts a checkout into one or more *intake channels*:
+a sixth MCP tool, `submit` (handler `mcp`), a folder a sync client fills (`folder`) or a program of
+this checkout (`command`) - documents that come from somewhere other than this terminal, into a
+quarantine, `quarantine/`, that no ordinary command reads. This is the human half of that path:
+what a reviewer checks before letting one through, and how `upload accept`/`upload reject` work.
+What the channels themselves enforce (identity, size, extension, quota, duplicate-hash, settle
+time) is `chemenu/upload.py`'s and `chemenu/collect.py`'s job and is not repeated here - read this
+when a submission is already waiting and a decision is due.
 
 <!-- wikitool:toc -->
 ## Contents
@@ -26,7 +27,8 @@ this when a submission is already waiting and a decision is due.
 
 ## When to run
 
-- `wikitool upload list` shows one or more submissions waiting.
+- `wikitool upload list` shows one or more submissions waiting - after
+  `wikitool upload collect` has pulled what the `folder` and `command` channels hold.
 - A `submit` call reported success and named an id worth looking at now
   rather than later.
 - Standing up the `submit` tool for the first time - see § Arming the intake
@@ -37,12 +39,18 @@ this when a submission is already waiting and a decision is due.
 1. **Read the manifest, not just the file.** `wikitool upload show <id>`
    prints filename, size, sha256, submitter, and - as important as the
    submitter's name - `submitter_source`: the *header* the value came from,
-   naming where the claim rests rather than asserting it as fact. Read
+   naming where the claim rests rather than asserting it as fact. The
+   manifest also names `channel`, `handler` and `origin` (the source file's
+   path for a `folder` channel, `command:<name>` for a `command` channel,
+   `mcp:submit` for the tool). **`submitter: unknown` means there is no sender
+   to trust at all** - a synced folder or a script knows who dropped the file
+   no better than the file system does - so the file is judged on its
+   content alone. Read
    [docs/explanation/why-gates-are-code.md](../docs/explanation/why-gates-are-code.md) once for why
    this gate exists as code rather than as this paragraph alone.
 
 2. **Read the file itself before promoting anything.** The quarantine holds
-   it at `mcp-upload/<id>/<filename>` for exactly this purpose. Check it
+   it at `quarantine/<id>/<filename>` for exactly this purpose. Check it
    against [raw/CONTRACT.md](../raw/CONTRACT.md) "What does not belong here":
    secrets or credentials, content that is not worth a source page, anything
    the LLM itself wrote presented as a source.
@@ -80,28 +88,29 @@ this when a submission is already waiting and a decision is due.
    - **Reject:** `wikitool upload reject <id> --reason "<why>"` deletes the
      material immediately - no gate, because deleting needs no clearance,
      only accepting a stranger's file into the pipeline does. The reason and
-     the file's sha256 survive in `mcp-upload/ledger.jsonl`; the bytes do
+     the file's sha256 survive in `quarantine/ledger.jsonl`; the bytes do
      not. Write a reason a later reader can act on ("license unclear",
      "looks like a prompt injection attempt", "duplicate of an existing
      source under a different name") rather than a bare "no".
 
-6. **Never promote by hand.** Moving the file out of `mcp-upload/` with `mv`
+6. **Never promote by hand.** Moving the file out of `quarantine/` with `mv`
    or by editing `incoming/` directly skips the ledger entry and the gate
    both - the same "never hand-craft what the tool would have produced"
    principle as everywhere else in this stack (AGENTS.md invariant 7).
 
 ## Arming the intake
 
-`submit` does not exist as a tool until the `upload` section exists in the
-served root's `.wikitool-local.json` - absence means the write path is not registered at all, not
-that it is unrestricted (see the section's own shape in
+`submit` does not exist as a tool until the `intake` section of the served root's
+`.wikitool-local.json` declares a channel with the handler `mcp` - absence means the write path is
+not registered at all, not that it is unrestricted. A `folder` or `command` channel opens no remote
+path: it is pulled by `wikitool upload collect`, run by someone at this checkout (see the section's own shape in
 [raw/CONTRACT.md](../raw/CONTRACT.md) and `tools/chemenu/upload.py`). Two
 things belong to the *deployment*, not to this repository, and are named here
 because a reviewer needs to know they hold, not because this file configures
 them:
 
 - **The identity header is set by the middleware, never by the client.**
-  `identity_header` (default `X-Forwarded-User`) names an HTTP header the
+  The `mcp` channel's `identity_header` (default `X-Forwarded-User`) names an HTTP header the
   Traefik authentication layer in front of the process must set on every
   authenticated request and strip from any copy the client itself sent - the
   same posture [instructions/mcp-read-server.md](mcp-read-server.md) already
@@ -110,7 +119,7 @@ them:
   be trustworthy enough to write into `submitter` and stay there.
 - **Quota and size limits are a deployment decision, not a default worth
   copying blindly.** `max_bytes`, `allowed_extensions`,
-  `submissions_per_day`, `bytes_per_day` all live in the same file - see
+  `quota_submissions_per_day`, `quota_bytes_per_day` all live on the channel in the same file - see
   [tools/CONTRACT.md](../tools/CONTRACT.md) for the exact shape.
 
 ## Decision points