@zalom/plastic 1.0.0-beta.8 → 1.0.0-beta.9

package/PLASTIC.md

@@ -50,6 +50,13 @@ tags: [plastic, architecture]
 - Context contract: load `sources` strongly (they are what the intent was built from);
   traverse `chain` lightly for discovery. See
   docs/concepts/how-plastic-sources-and-chains-intents.md for the full model.
+- `## Links` (I5) is the human-readable projection of the graph. It mirrors the
+  frontmatter exactly: every entry is `- [[id--slug|<target's full intent: text>]]`, a
+  clickable `id--slug` wikilink target with the target intent's full `intent:` text as the
+  label (cross-store targets render `- [[store:id--slug|<target's full intent: text>]]`).
+  Ordering is mandatory: all `sources` first (top), then all `chain`, frontmatter order
+  preserved within each group. Sources never appear at the end. No source/chain tags, no
+  sub-grouping. An intent with empty `sources` and `chain` carries the empty-state comment.
 - IDs use Luhmann's alternating convention: `1` → `1a` → `1a1` → `1a1a`
 - Multiple branches increment: `1a`, `1b`, `1c`
 
@@ -164,8 +171,8 @@ Format: `ID--three-to-five-words` (all stores).
 - **Root (`15`, `16`)**: an independent thought, even if inspired by another intent.
   Reserve `sources` for true created-from provenance (intents this was built out of). An
   independent intent merely related to or inspired by another carries NO `sources`; record
-  the relation on the PREDECESSOR's `chain` (and mirror it as a `[[id]]` wikilink in
-  `## Links`).
+  the relation on the PREDECESSOR's `chain` (and mirror it as a
+  `[[id--slug|<target's full intent: text>]]` wikilink in `## Links`).
 - **Rule of thumb:** if the intent could exist without its parent, it's a root.
 
 ## INDEX.md

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@zalom/plastic",
-  "version": "1.0.0-beta.8",
+  "version": "1.0.0-beta.9",
   "description": "Intent-driven idea development system for AI coding agents",
   "type": "module",
   "bin": {

package/scripts/doctor.rb

@@ -17,6 +17,9 @@ require "digest"
 
 require_relative "lib/qmd_sync"
 require_relative "lib/intent_validator"
+require_relative "lib/graph_rebuild"
+require_relative "lib/links_projection"
+require_relative "lib/links_section"
 
 # Diagnostic engine, instantiable with an injected store/agent map so tests can
 # run it hermetically (no eval, no global-constant rewriting).
@@ -480,9 +483,178 @@ class Doctor
     # flagged: validate_graph does not compute it.
     checks.concat(graph_invariant_checks(intent_dirs))
 
+    # cross_store_resolution — RESOLVES (not just shape-checks) every cross-store
+    # `store:id` ref against the FULL store family via the relocation map
+    # (relocation consulted first), closing the shape-only gap i1/i3/i4 leave open.
+    # Resolution always spans all stores even under `--store` scoping; only the
+    # REPORTED findings are filtered to refs originating in the scoped store(s).
+    checks << cross_store_resolution_check(scopes: scopes)
+
+    # graph_links_projection — the `## Links` section of every intent must EQUAL its
+    # canonical I5 frontmatter projection (intent 72), in BOTH set membership AND
+    # ordering (sources first, then chain). Recomputes the projection from each
+    # intent's sources/chain + the on-disk basenames using the SAME resolver the
+    # scripts/project-links tool uses, so the two can never diverge. Resolution
+    # spans all stores; only the REPORTED findings are filtered to the scoped store.
+    checks << links_projection_check(scopes: scopes)
+
     checks
   end
 
+  # Build the cross-store node maps (basename + label per store) + relocation map
+  # from ALL stores, then for every intent compute its canonical `## Links`
+  # projection and flag any whose ACTUAL `## Links` section differs (membership or
+  # ordering drift), or whose projection raises UnresolvedRef. `scopes` (nil = full
+  # run) filters only the REPORTED findings by origin scope.
+  def links_projection_check(scopes: nil)
+    all_dirs = all_intent_dirs
+
+    store_index = Hash.new { |h, k| h[k] = [] }
+    node_index = Hash.new { |h, k| h[k] = {} }
+    intents = [] # { scope:, id:, sources:, chain:, path: }
+
+    all_dirs.each do |d|
+      md = File.join(d[:path], "#{d[:name]}.md")
+      next unless File.exist?(md)
+
+      fm = parse_frontmatter(md)
+      next unless fm.is_a?(Hash) && fm["id"]
+
+      id = fm["id"].to_s
+      store_index[d[:scope]] << id
+      node_index[d[:scope]][id] = { basename: d[:name], label: fm["intent"].to_s.strip }
+      intents << {
+        scope: d[:scope], id: id, path: md,
+        sources: Array(fm["sources"]).map(&:to_s),
+        chain: Array(fm["chain"]).map(&:to_s),
+      }
+    end
+
+    relocation_map = GraphRebuild.build_relocation_map(cross_store_index_texts)
+
+    findings = []
+    intents.each do |node|
+      next if scopes && !scopes.include?(node[:scope])
+
+      resolve = ->(ref) do
+        LinksProjection.resolve_ref_projection(
+          ref, referer_store: node[:scope],
+               relocation_map: relocation_map, store_index: store_index, node_index: node_index
+        )
+      end
+
+      begin
+        expected = LinksProjection.section(sources: node[:sources], chain: node[:chain], resolve: resolve)
+        actual = actual_links_section(node[:path])
+      rescue LinksProjection::UnresolvedRef => e
+        findings << "#{node[:id]} ## Links projection failed: #{e.message}"
+        next
+      rescue LinksSection::AmbiguousLinks => e
+        findings << "#{node[:id]} ## Links ambiguous: #{e.message}"
+        next
+      end
+
+      next if actual == expected
+
+      findings << "#{node[:id]} ## Links does not match its frontmatter projection (membership/ordering drift)"
+    end
+
+    graph_finding_check(
+      "graph_links_projection", findings,
+      "Every intent's ## Links equals its frontmatter projection (membership and ordering)",
+      "Run scripts/project-links to regenerate the canonical ## Links sections"
+    )
+  end
+
+  # Extract a file's ACTUAL REAL `## Links` section text (FENCE-AWARE), normalized
+  # to the canonical block shape the projection emits. Delegates to the shared
+  # LinksSection.extract_section so the doctor check and the project-links tool
+  # agree on the section location and never match a `## Links` heading inside an
+  # example code fence. Returns "" when the section is absent (which differs from
+  # any real projection, so a missing section is a finding).
+  def actual_links_section(path)
+    LinksSection.extract_section(IntentValidator.body_of(File.read(path)))
+  end
+
+  # Build the relocation map + cross-store store_index from ALL stores, then for
+  # every intent's cross-store `sources`/`chain` ref resolve it and flag:
+  #   - DEAD: the target resolves nowhere
+  #   - RELOCATED-STALE: the ref points at an old location the relocation log has
+  #     moved (the resolved location differs from the literal ref), e.g. the
+  #     `global:24` id-reuse hazard that direct resolution would silently accept.
+  # `scopes` (nil = full run) filters only the REPORTED findings by origin scope.
+  def cross_store_resolution_check(scopes: nil)
+    all_dirs = all_intent_dirs
+
+    # Per-scope node maps + store_index over the WHOLE family.
+    nodes_by_scope = Hash.new { |h, k| h[k] = {} }
+    store_index = Hash.new { |h, k| h[k] = [] }
+    all_dirs.each do |d|
+      md = File.join(d[:path], "#{d[:name]}.md")
+      next unless File.exist?(md)
+
+      fm = parse_frontmatter(md)
+      next unless fm.is_a?(Hash) && fm["id"]
+
+      id = fm["id"].to_s
+      store_index[d[:scope]] << id
+      nodes_by_scope[d[:scope]][id] = {
+        sources: Array(fm["sources"]).map(&:to_s),
+        chain: Array(fm["chain"]).map(&:to_s),
+      }
+    end
+
+    relocation_map = GraphRebuild.build_relocation_map(cross_store_index_texts)
+
+    findings = []
+    nodes_by_scope.each do |scope, nodes|
+      next if scopes && !scopes.include?(scope)
+
+      nodes.each do |id, edges|
+        %i[sources chain].each do |field|
+          edges[field].each do |ref|
+            next unless ref.include?(":") # only cross-store refs are resolved here
+
+            res = GraphRebuild.resolve_ref(ref, referer_store: scope,
+                                                relocation_map: relocation_map,
+                                                store_index: store_index)
+            case res[:status]
+            when :dead
+              findings << "#{id}.#{field} cross-store ref #{ref} resolves to no intent (dead)"
+            when :same_store
+              findings << "#{id}.#{field} cross-store ref #{ref} is relocated-stale (now same-store #{res[:id]})"
+            when :cross_store
+              findings << "#{id}.#{field} cross-store ref #{ref} is relocated-stale (now #{res[:ref]})" if res[:ref] != ref
+            end
+          end
+        end
+      end
+    end
+
+    graph_finding_check(
+      "graph_cross_store_resolution", findings,
+      "Every cross-store sources/chain ref resolves to a live, current intent",
+      "Run scripts/rebuild-graph to repoint/collapse/drop stale cross-store refs"
+    )
+  end
+
+  # { store_key => INDEX.md text } for every store (global + all projects), for the
+  # relocation-map builder. Reads INDEX.md one level above each store dir.
+  def cross_store_index_texts
+    texts = {}
+    global_index = File.join(plastic_home, "INDEX.md")
+    texts["global"] = File.read(global_index) if File.exist?(global_index)
+
+    projects_root = File.join(plastic_home, "projects")
+    if File.directory?(projects_root)
+      Dir.children(projects_root).each do |project|
+        idx = File.join(projects_root, project, "INDEX.md")
+        texts["project:#{project}"] = File.read(idx) if File.exist?(idx)
+      end
+    end
+    texts
+  end
+
   # Build a per-scope `nodes` map and surface IntentValidator.validate_graph
   # findings as warn-level checks. Scope-aware (the caller already filtered
   # `intent_dirs` by scope), so a `global` id is not falsely flagged as a dangler

package/scripts/lib/frontmatter_writer.rb

@@ -0,0 +1,130 @@
+# encoding: UTF-8
+# frozen_string_literal: true
+
+# FrontmatterWriter — pure, minimal, style-preserving rewrite of the `sources:`
+# and `chain:` arrays in an intent file's content string (intent 49).
+#
+# It rewrites ONLY those two arrays and leaves every other frontmatter line and
+# the entire body byte-identical. It preserves each array's existing serialization
+# style independently:
+#   - flow style: `sources: ["40", "1a"]`  (or `[]`)
+#   - block style: a `sources:` line followed by `  - '1a'` item lines
+# When the desired array equals the file's current value (same ids, same order),
+# the content is returned UNCHANGED so a re-run produces no diff (idempotency).
+#
+# Pure: no file IO, no eval, no global/ENV state. The IO shell reads/writes files.
+module FrontmatterWriter
+  module_function
+
+  # Rewrite `sources:`/`chain:` in `content`. `sources`/`chain` are the desired
+  # final arrays of id strings. Returns the new content (or the original when
+  # nothing changed). Only operates within the leading `---`...`---` frontmatter
+  # block; never touches the body.
+  def rewrite_arrays(content, sources:, chain:)
+    return content unless content.is_a?(String) && content.start_with?("---")
+
+    parts = content.split("---", 3)
+    return content if parts.length < 3
+
+    fm = parts[1]
+    body = parts[2]
+
+    fm = rewrite_one(fm, "sources", sources)
+    fm = rewrite_one(fm, "chain", chain)
+
+    "---#{fm}---#{body}"
+  end
+
+  # Rewrite a single `key:` array within the frontmatter text `fm`, preserving the
+  # key's existing flow-vs-block style. No-op when the key is absent or unchanged.
+  def rewrite_one(fm, key, desired)
+    lines = fm.lines
+    idx = lines.index { |l| l.match?(/\A#{Regexp.escape(key)}:\s/) || l.match?(/\A#{Regexp.escape(key)}:\s*\z/) }
+    return fm if idx.nil?
+
+    header = lines[idx]
+    if block_style?(lines, idx)
+      rewrite_block(lines, idx, key, desired)
+    else
+      rewrite_flow(lines, idx, header, key, desired)
+    end
+  end
+
+  # The key is block style when its own line carries no inline value and the next
+  # non-blank line is a `-` list item.
+  def block_style?(lines, idx)
+    header = lines[idx]
+    inline = header.sub(/\A[^:]+:/, "").strip
+    return false unless inline.empty?
+
+    nxt = lines[idx + 1]
+    !nxt.nil? && nxt.match?(/\A\s*-\s/)
+  end
+
+  # Flow style: replace the inline array on the header line, preserving indentation
+  # and any trailing newline. No-op when the current ids already match `desired`.
+  def rewrite_flow(lines, idx, header, key, desired)
+    current = parse_flow(header)
+    return lines.join if current == desired
+
+    newline = header.end_with?("\n") ? "\n" : ""
+    lines[idx] = "#{key}: #{render_flow(desired)}#{newline}"
+    lines.join
+  end
+
+  # Parse the inline flow array from a `key: [ ... ]` header line.
+  def parse_flow(header)
+    inline = header.sub(/\A[^:]+:/, "").strip
+    return [] if inline.empty? || inline == "[]"
+
+    inline = inline.sub(/\A\[/, "").sub(/\]\z/, "")
+    inline.split(",").map { |t| t.strip.gsub(/\A['"]|['"]\z/, "") }.reject(&:empty?)
+  end
+
+  def render_flow(ids)
+    return "[]" if ids.empty?
+
+    "[#{ids.map { |i| "\"#{i}\"" }.join(", ")}]"
+  end
+
+  # Block style: replace the contiguous `-` item lines following the header. No-op
+  # when the current ids already match `desired`. Preserves the item indentation
+  # and quoting style sampled from the existing first item.
+  def rewrite_block(lines, idx, key, desired)
+    last = idx
+    item_lines = []
+    (idx + 1).upto(lines.length - 1) do |i|
+      break unless lines[i].match?(/\A\s*-\s/)
+
+      item_lines << lines[i]
+      last = i
+    end
+
+    current = item_lines.map { |l| l.sub(/\A\s*-\s*/, "").strip.gsub(/\A['"]|['"]\z/, "") }
+    return lines.join if current == desired
+
+    indent, quote = block_item_shape(item_lines.first)
+    rendered = desired.map { |id| "#{indent}- #{quote}#{id}#{quote}\n" }
+
+    # When desired is empty, collapse the block to an inline `key: []` to keep YAML
+    # valid (a bare `key:` with no items parses as nil, not an empty array).
+    rendered = ["#{key}: []\n"] if desired.empty? && rendered.empty?
+
+    if desired.empty?
+      new_lines = lines[0...idx] + rendered + lines[(last + 1)..]
+    else
+      new_lines = lines[0...idx] + [lines[idx]] + rendered + lines[(last + 1)..]
+    end
+    new_lines.join
+  end
+
+  # Sample indentation and quote char from an existing block item line.
+  def block_item_shape(sample)
+    return ["", "'"] if sample.nil?
+
+    indent = sample[/\A\s*/].to_s
+    value = sample.sub(/\A\s*-\s*/, "").strip
+    quote = value.start_with?('"') ? '"' : "'"
+    [indent, quote]
+  end
+end

package/scripts/lib/graph_rebuild.rb

@@ -0,0 +1,328 @@
+# encoding: UTF-8
+# frozen_string_literal: true
+
+# GraphRebuild — pure logic for repairing the store-wide sources/chain graph
+# (intent 49). Mirrors the pure-module style of IntentValidator: module-function
+# helpers with no file IO. The IO shell (scripts/rebuild-graph) and doctor build
+# the in-memory maps and feed them here.
+#
+# Two concerns live here:
+#   1. Cross-store relocation. Each store's INDEX.md `## Relocated` log records
+#      moves like `global:24 → project:22c` (or backtick bare-id form `1b1a1 → 41`).
+#      build_relocation_map parses every log into a multi-hop-collapsed map; the
+#      resolver consults it BEFORE direct id resolution so a relocation always wins
+#      over a coincidentally-reused id (the `global:24` impostor hazard).
+#   2. The per-intent rebuild transform (intent 68 I-invariants, one-directional):
+#      dedupe -> I3 (formative edge wins) -> cross-store resolve -> I1 backlinks ->
+#      I2 preserved (relational chains survive).
+module GraphRebuild
+  module_function
+
+  RELOCATION_ARROW = "→" # the unicode → used in every Relocated log
+
+  # PURE. Parse every store's INDEX.md `## Relocated` block into a multi-hop
+  # relocation map.
+  #
+  # `index_texts` is { store_key => index_md_string } where store_key is "global"
+  # or "project:<slug>". Returns { [from_store, from_id] => [to_store, to_id] }
+  # with chains transitively collapsed to their final hop. The `to_store` token is
+  # NORMALIZED: the generic `project:` token in the global log is left as the
+  # literal it appears with; resolve_ref maps a same-family target to a bare id.
+  #
+  # Two real arrow forms are handled:
+  #   - `global:24 → project:22c`   (store-prefixed, global log)
+  #   - `1b1a1 → 41` inside backticks (bare ids, plastic log) — these are
+  #     same-store moves; from/to store both default to the store the log lives in.
+  def build_relocation_map(index_texts)
+    raw = {}
+    (index_texts || {}).each do |store_key, text|
+      next unless text.is_a?(String)
+
+      relocated_block(text).each_line do |line|
+        parse_relocation_line(line, store_key).each do |(from, to)|
+          raw[from] = to
+        end
+      end
+    end
+    collapse_multi_hop(raw)
+  end
+
+  # Extract the text of the `## Relocated` section (everything from the heading to
+  # the next top-level `## ` heading or EOF). Returns "" when absent.
+  def relocated_block(text)
+    lines = text.lines
+    start = lines.index { |l| l.strip == "## Relocated" }
+    return "" if start.nil?
+
+    rest = lines[(start + 1)..] || []
+    stop = rest.index { |l| l.start_with?("## ") }
+    (stop ? rest[0...stop] : rest).join
+  end
+
+  # Parse one log line into an array of [[from_store, from_id], [to_store, to_id]]
+  # pairs. A line may pack several comma-separated pairs and carry trailing prose
+  # in parens. Lines without an arrow yield []. `home_store` is the store whose
+  # log this line came from (used as the default store for bare ids).
+  def parse_relocation_line(line, home_store)
+    body = line.sub(/\A\s*-\s*/, "") # drop list bullet
+    return [] unless body.include?(RELOCATION_ARROW)
+
+    body.split(",").filter_map do |segment|
+      seg = segment.strip
+      next nil unless seg.include?(RELOCATION_ARROW)
+
+      left, right = seg.split(RELOCATION_ARROW, 2)
+      from = parse_token(left, home_store)
+      to = parse_token(right, home_store)
+      next nil if from.nil? || to.nil?
+
+      [from, to]
+    end
+  end
+
+  # Parse a single `store:id` / bare-id token (possibly wrapped in backticks or
+  # trailed by parenthetical prose) into [store_key, bare_id], or nil. A bare id
+  # defaults to `home_store`. The generic `project:` prefix is resolved later by
+  # resolve_ref against the referer's store family; here it is recorded literally.
+  def parse_token(token, home_store)
+    cleaned = token.to_s.tr("`", " ").strip
+    cleaned = cleaned.sub(/\s*\(.*\z/, "").strip # drop trailing "(prose"
+    cleaned = cleaned.split(/\s/).first.to_s     # first whitespace-delimited atom
+    return nil if cleaned.empty?
+
+    if cleaned.include?(":")
+      store_tok, id = cleaned.split(":", 2)
+      return nil if id.to_s.empty?
+
+      [normalize_store_token(store_tok), id]
+    else
+      [home_store, cleaned]
+    end
+  end
+
+  # Normalize a store token from a log to a store_key. "global" stays "global".
+  # The generic "project" token (used in the global log) is kept as the sentinel
+  # "project" — resolve_ref binds it to the referer's project family.
+  def normalize_store_token(tok)
+    t = tok.to_s.strip
+    t == "global" ? "global" : t
+  end
+
+  # Transitively collapse a → b → c chains so every key maps to its FINAL hop.
+  # Cycle-guarded. Keys/values are [store_key, id] pairs.
+  def collapse_multi_hop(raw)
+    raw.each_with_object({}) do |(from, _to), acc|
+      seen = [from]
+      cur = raw[from]
+      while cur && raw.key?(cur) && !seen.include?(cur)
+        seen << cur
+        cur = raw[cur]
+      end
+      acc[from] = cur
+    end
+  end
+
+  # PURE. Resolve a single ref (a `store:id` cross-store ref, or a bare same-store
+  # id) to a final location and classification. ORDER IS LOAD-BEARING: the
+  # relocation map is consulted FIRST, so a relocation wins over a coincidentally
+  # reused id.
+  #
+  #   ref             — "global:24" or "22c"
+  #   referer_store   — store_key of the intent carrying the ref ("global"/"project:plastic")
+  #   relocation_map  — from build_relocation_map
+  #   store_index     — { store_key => Array/Set of bare ids present in that store }
+  #
+  # Returns a Hash:
+  #   { status: :same_store, id: "<bare id>" }              -> collapse to bare id
+  #   { status: :cross_store, ref: "<store>:<id>" }         -> keep/repoint store:id
+  #   { status: :dead, ref: <original> }                    -> drop (resolves nowhere)
+  def resolve_ref(ref, referer_store:, relocation_map:, store_index:)
+    store_tok, bare = split_ref(ref, referer_store)
+
+    # 1) Relocation FIRST. Look up [store, id]; the generic "project" target token
+    #    is bound to the referer's family when emitting the location.
+    reloc_key = [store_tok, bare]
+    if (relocation_map || {}).key?(reloc_key)
+      to_store, to_id = relocation_map[reloc_key]
+      to_store = bind_project_token(to_store, referer_store, store_index, to_id)
+      return classify(to_store, to_id, referer_store, store_index, ref)
+    end
+
+    # 2) Direct resolution against the live store index.
+    classify(store_tok, bare, referer_store, store_index, ref)
+  end
+
+  # Split a ref into [store_key, bare_id]; bare refs take the referer's store.
+  def split_ref(ref, referer_store)
+    s = ref.to_s
+    if s.include?(":")
+      store_tok, id = s.split(":", 2)
+      [normalize_store_token(store_tok), id]
+    else
+      [referer_store, s]
+    end
+  end
+
+  # The global log writes relocation targets as the generic `project:` token. Bind
+  # it to the concrete store family that actually owns the bare id. Prefer the
+  # referer's store when it holds the id; otherwise pick any store that has it.
+  def bind_project_token(to_store, referer_store, store_index, to_id)
+    return to_store unless to_store == "project"
+
+    return referer_store if ids_in(store_index, referer_store).include?(to_id)
+
+    owner = (store_index || {}).keys.find { |k| ids_in(store_index, k).include?(to_id) }
+    owner || referer_store
+  end
+
+  # Map a ref store token to the canonical store_index key. Refs in frontmatter
+  # use the slug form (`global`, `knowdb`, `plastic`); store_index keys use
+  # `global` and `project:<slug>`. "global" is canonical; anything else maps to
+  # `project:<token>` when that key exists, else the token itself (it may already
+  # be a `project:<slug>` key, e.g. a relocation target).
+  def canonical_store_key(store_tok, store_index)
+    return store_tok if store_tok == "global"
+    return store_tok if (store_index || {}).key?(store_tok)
+
+    projected = "project:#{store_tok}"
+    (store_index || {}).key?(projected) ? projected : store_tok
+  end
+
+  # The slug form of a canonical store key, for emitting a cross-store `slug:id`
+  # ref (the form used in frontmatter). "global" stays "global"; "project:<slug>"
+  # becomes "<slug>".
+  def slug_of(canonical_key)
+    canonical_key.to_s.sub(/\Aproject:/, "")
+  end
+
+  # Classify a resolved (store, id) relative to the referer, using the live store
+  # index to detect dead targets:
+  #   - target id present in the referer's OWN store -> :same_store (collapse to bare)
+  #   - target id present in a DIFFERENT store       -> :cross_store (keep slug:id)
+  #   - target id present NOWHERE                     -> :dead (drop)
+  def classify(store_tok, bare, referer_store, store_index, original_ref)
+    canonical = canonical_store_key(store_tok, store_index)
+    if ids_in(store_index, canonical).include?(bare)
+      if canonical == referer_store
+        { status: :same_store, id: bare }
+      else
+        { status: :cross_store, ref: "#{slug_of(canonical)}:#{bare}" }
+      end
+    else
+      { status: :dead, ref: original_ref.to_s }
+    end
+  end
+
+  def ids_in(store_index, store_key)
+    Array((store_index || {})[store_key])
+  end
+
+  # PURE. Per-store rebuild transform (intent 68 I-invariants, one-directional).
+  # Deterministic and idempotent: a second call over the result yields zero changes.
+  #
+  #   nodes          — ONE store's { id => { sources: [...], chain: [...] } } map
+  #   referer_store  — that store's key ("global" / "project:<slug>")
+  #   relocation_map — from build_relocation_map (spans all stores)
+  #   store_index    — { store_key => bare ids present } (spans all stores)
+  #
+  # Returns { nodes: <new map>, changes: [ {intent:, kind:, before:, after:} ] }.
+  # kinds: :dedupe, :i3, :repoint, :collapse, :drop, :i1_backlink.
+  #
+  # Order is load-bearing (spec Phase 2):
+  #   1. dedupe each array order-preserving
+  #   2. I3: an id in BOTH sources and chain is kept in sources, dropped from chain
+  #   3. cross-store resolve each ref (relocation FIRST): repoint, collapse to bare
+  #      same-store, or drop dead
+  #   4. I1: for every in-store source s, ensure s.chain backlinks this intent
+  #   5. I2 preserved: never synthesize a reciprocal source, never strip a
+  #      relational chain entry
+  def rebuild_store(nodes, referer_store:, relocation_map:, store_index:)
+    out = {}
+    (nodes || {}).each do |id, edges|
+      edges = {} unless edges.is_a?(Hash)
+      out[id.to_s] = {
+        sources: Array(edges[:sources] || edges["sources"]).map(&:to_s),
+        chain: Array(edges[:chain] || edges["chain"]).map(&:to_s),
+      }
+    end
+
+    changes = []
+
+    out.each do |id, edges|
+      # 1. dedupe order-preserving
+      deduped_sources = edges[:sources].uniq
+      deduped_chain = edges[:chain].uniq
+      if deduped_sources != edges[:sources] || deduped_chain != edges[:chain]
+        changes << { intent: id, kind: :dedupe,
+                     before: { sources: edges[:sources].dup, chain: edges[:chain].dup },
+                     after: { sources: deduped_sources, chain: deduped_chain } }
+      end
+      edges[:sources] = deduped_sources
+      edges[:chain] = deduped_chain
+
+      # 2. I3: overlap kept in sources, dropped from chain
+      overlap = edges[:sources] & edges[:chain]
+      overlap.each do |o|
+        changes << { intent: id, kind: :i3, before: o, after: nil }
+      end
+      edges[:chain] -= overlap unless overlap.empty?
+
+      # 3. cross-store resolve sources and chain
+      %i[sources chain].each do |field|
+        rebuilt = []
+        edges[field].each do |ref|
+          unless ref.include?(":")
+            rebuilt << ref # bare same-store id, left as-is here (I4 is doctor's job)
+            next
+          end
+
+          res = resolve_ref(ref, referer_store: referer_store,
+                                 relocation_map: relocation_map, store_index: store_index)
+          case res[:status]
+          when :same_store
+            if res[:id] != ref
+              changes << { intent: id, kind: :collapse, field: field, before: ref, after: res[:id] }
+            end
+            rebuilt << res[:id]
+          when :cross_store
+            if res[:ref] != ref
+              changes << { intent: id, kind: :repoint, field: field, before: ref, after: res[:ref] }
+            end
+            rebuilt << res[:ref]
+          when :dead
+            changes << { intent: id, kind: :drop, field: field, before: ref, after: nil }
+            # dropped: not appended
+          end
+        end
+        # de-dupe again after collapse/repoint may have created duplicates
+        edges[field] = rebuilt.uniq
+      end
+
+      # 3b. Re-apply I3 AFTER resolution: a cross-store ref that collapses to a
+      #     bare same-store id can newly overlap an existing chain entry (e.g.
+      #     sources:[global:14a]→[19a] meeting chain:[19a]). Formative edge wins.
+      post_overlap = edges[:sources] & edges[:chain]
+      post_overlap.each do |o|
+        changes << { intent: id, kind: :i3, before: o, after: nil }
+      end
+      edges[:chain] -= post_overlap unless post_overlap.empty?
+    end
+
+    # 4. I1: in-store source backlinks (mutates OTHER nodes). Runs after resolution
+    #    so collapsed bare ids participate. Order-preserving append.
+    out.each do |id, edges|
+      edges[:sources].each do |s|
+        next if s.include?(":")        # cross-store: backlink lives in another store
+        next unless out.key?(s)        # unresolved bare id is an I4 dangler, not I1
+        next if out[s][:chain].include?(id)
+
+        before_chain = out[s][:chain].dup
+        out[s][:chain] = out[s][:chain] + [id]
+        changes << { intent: s, kind: :i1_backlink, field: :chain,
+                     before: before_chain, after: out[s][:chain].dup, backlink: id }
+      end
+    end
+
+    { nodes: out, changes: changes }
+  end
+end