Make janook citable, current, and shown working - #53
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The documentation epic, minus the website the owner descoped: the repo is the one source of truth, and janook.org will simply point here. The README now passes its thirty-second test: the real classify output sits near the top, an Install section describes the release archive that actually works today (with the conda line arriving when Bioconda merges), and Status tells the truth - 9.0.0 released, validate coming, one sentence on why it waits. The stale from-a-clone note is fixed. CITATION.cff makes 'as implemented in janook v9.0.0' resolvable, and the Citing section keeps the two citations apart: the paper for the standard, janook for the implementation. The cff credits The Janook Authors and names no individual, consistent with the copyright decision. The worked example goes public in examples/pkd1: the evidence file with honest reasoning, the real outputs, and a narration of why rule P.i fired. A test parses and classifies the committed file on every build, so the example cannot drift from the tool - the same rule that keeps the criteria reference and the init template honest. Authored by itpragmatik and an AI agent
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The documentation epic's three stories in one PR, with the website descoped per the owner's decision — the repo is the single source of documentation truth, and
janook.orgbecomes a redirect (DNS flip pending, owner's Route 53).The README passes its thirty-second test. The real
classifyoutput sits near the top — the fastest honest answer to "what does this do" — followed by an Install section describing exactly what works today (the release archive; theconda installline arrives when Bioconda merges, and the section says so without printing a command that does not work yet). Status catches up twice over: 9.0.0 released, everything working end to end, andvalidatenamed as coming with one sentence on why it waits. The stale "there is no installable janook yet" note is gone.CITATION.cff+ a Citing section. GitHub's cite button now works; the section holds the line the whole project holds — two citations for two different things, the paper (exact title verified against Crossref) for the standard, janook-at-a-version for the implementation, with the one-sentence methods example a paper actually needs. The cff credits "The Janook Authors" and names no individual, consistent with the copyright decision.The worked example goes public in
examples/pkd1/: the PKD1 evidence file with honest reasoning and citations, all four outputs shown as actually produced, and a plain narration of the decision path — including why branch B running and finding nothing matters.WorkedExampleTestparses and classifies the committed file on every build, so the example cannot drift from the tool: the honest-template rule, applied a third time.mvn clean verifygreen, public-safety and dist checks pass. Merging on green CI per the owner's instruction.