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docs: Methods & Tools redesign implementation plan#1172

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docs: Methods & Tools redesign implementation plan#1172
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Phased, grounded implementation plan for the Methods & Tools redesign (#1166/#1167/#1168), referenced by those re-scoped issues and #1158.

Corrects the earlier handoff's drift (no mark-term.tsx/markTermInText, no PR #1164; the interim highlight is in the publication modal, not the profile panel), records that Surface B's entity layer is net-new (not a reframe), and sequences the work:

Docs-only. Follows the #1169 precedent (spec + mockups + handoff).

Phased, grounded implementation plan for the Methods & Tools redesign
(#1166/#1167/#1168). Corrects the earlier handoff's drift (the highlighter
and PR #1164 do not exist on master; the interim work is in the publication
modal, not the profile panel), records that Surface B's entity layer is
net-new rather than a reframe, and sequences the work: Phase 1 ships against
the existing tool/family grain (source pmid + shared provenance rail +
Surface A), Phase 2 is the #1166 gate (new family_entity_usage table + the
ReciterAI entity-resolution stage), Phase 3 is full Surface B discovery.

Referenced by the re-scoped #1166/#1167/#1168/#1158.
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