feat: incoming/ as a queue - raw pending picks the next entry, raw accept takes a whole folder, a file in a subdirectory of incoming/ is refused (#112)

Files changed:
- CHANGES.md
- README.md
- VERSION
- instructions/ingest-large-tree.md
- instructions/wiki-ingest/SKILL.md
- raw/CONTRACT.md
- tools/CONTRACT.md
- tools/chemenu/cli_contract.py
- tools/chemenu/commands/raw_cmd.py
- tools/chemenu/tests/test_raw_cmd.py
- tools/chemenu/tests/test_raw_fetch.py

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2

README.md

@@ -90,7 +90,7 @@ chemenu/
 ├── mcp-upload/         # QUARANTINE (optional): the MCP `submit` tool's write path, gitignored -
 │                       #   read by no command in the ordinary pipeline; a human reviews it with
 │                       #   `wikitool upload list/show/accept/reject`
-├── incoming/           # INBOX: flat, content gitignored - drop a file here, `raw accept` promotes it
+├── incoming/           # INBOX: content gitignored - drop a file or one folder per source here, `raw accept` promotes it
 ├── raw/                # INPUT: immutable, untrusted source material
 │   ├── CONTRACT.md     # Date shard, capture fields, immutability, untrusted content
 │   ├── 2026/09/        # Where `raw accept` puts a file: the month it was accepted
@@ -185,12 +185,14 @@ working *with* it.
 
 ### Adding Knowledge (Ingest)
 
-1. Drop a file into `incoming/` - flat, no classification to make. Everything past that
-   (the destination in `raw/`, which is a `YYYY/MM` shard of the day it was accepted,
-   and whether several files of one source get bundled) is computed by
-   `tools/wikitool raw accept`, never chosen by hand
-2. Tell the LLM: `Ingest incoming/my-article.md`. It will ask you two things before
-   promoting: how faithful the capture is (`fidelity`) and what the material may claim
+1. Drop a file into `incoming/` - directly, no classification to make. Files that belong
+   together go into one folder there instead: a folder is one source, accepted whole with
+   its structure kept. Everything past that (the destination in `raw/`, which is a `YYYY/MM`
+   shard of the day it was accepted, and whether several files of one source get bundled)
+   is computed by `tools/wikitool raw accept`, never chosen by hand
+2. Tell the LLM: `Ingest incoming/my-article.md` - or just `Ingest`, which takes the oldest
+   entry waiting in `incoming/` (`tools/wikitool raw pending` lists them). It will ask you
+   two things before promoting: how faithful the capture is (`fidelity`) and what the material may claim
    about its subject (`authority`). Both are recorded once and never guessed - they are
    knowable now and unrecoverable later
 3. The LLM will:
@@ -285,7 +287,8 @@ tools/wikitool types describe entity
 
 ### For You (Human)
 
-1. **Curate sources** - Drop files you want processed into `incoming/` (flat)
+1. **Curate sources** - Drop files you want processed into `incoming/` - directly, or one folder
+   per source
 2. **Ask questions** - Query the wiki naturally
 3. **Review changes** - Check `kb/log.md` and `kb/index.md`
 4. **Direct the LLM** - Guide it on what to emphasize or investigate