organize-wiki

1# Organize Wiki
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3Keep the user's paper library in domain folders they agree with. You **propose**, with evidence from the library and their research memory; the user decides. Only a confirmed plan reaches the vault, only through `scripts/organize.py`, and only after the user has seen its preview.
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5`references/file-contract.md` defines the library layout, the domains file, the scan, the plan, and the log. Read it before step 3.
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7To undo the last reorganization, run `python3 scripts/organize.py undo --latest`, report what it restored or the conflicts it lists, and stop.
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9## 1. Read the library
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11Run `python3 scripts/scan_library.py --output <tmp>/scan.json`. It finds the vault through DeepPaperNote's configuration. On `needs_vault` or `not_a_vault`, ask the user once for their Obsidian vault folder and pass `--vault <path>` to every script.
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13**Done when** the scan reports `status: ok`.
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15## 2. Agree on the convention
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17The **convention** is the set of domains, each with a definition, what it includes, what it excludes and where that goes instead, and three to five representative papers. `domains_file.exists` picks the mode.
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19**Building** (no domains file): draft each existing domain's fields from its papers' titles and excerpts, then propose changes to the set:
20- merge a domain holding one or two papers, or two domains whose papers mostly overlap;
21- split a domain past about 25 papers that holds at least two clear sub-areas of five or more papers each;
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