Graph

# Count total notes (excluding MOCs)
NOTES_DIR="{vocabulary.notes}"
TOTAL=$(ls -1 "$NOTES_DIR"/*.md 2>/dev/null | wc -l | tr -d ' ')
MOC_COUNT=$(grep -rl '^type: moc' "$NOTES_DIR"/*.md 2>/dev/null | wc -l | tr -d ' ')
NOTE_COUNT=$((TOTAL - MOC_COUNT))

# Count all wiki links
LINK_COUNT=$(grep -ohP '\[\[[^\]]+\]\]' "$NOTES_DIR"/*.md 2>/dev/null | wc -l | tr -d ' ')

# Calculate link density
# Density = actual_links / possible_links
# possible_links = N * (N - 1) for directed graph
echo "Density: $LINK_COUNT / ($NOTE_COUNT * ($NOTE_COUNT - 1))"

# Find orphan notes (zero incoming links)
for f in "$NOTES_DIR"/*.md; do
  NAME=$(basename "$f" .md)
  INCOMING=$(grep -rl "\[\[$NAME\]\]" "$NOTES_DIR"/ 2>/dev/null | grep -v "$f" | wc -l | tr -d ' ')
  [[ "$INCOMING" -eq 0 ]] && echo "ORPHAN: $NAME"
done

# Find dangling links (links to non-existent files)
grep -ohP '\[\[([^\]]+)\]\]' "$NOTES_DIR"/*.md 2>/dev/null | sort -u | while read -r link; do
  NAME=$(echo "$link" | sed 's/\[\[//;s/\]\]//')
  [[ ! -f "$NOTES_DIR/$NAME.md" ]] && echo "DANGLING: $NAME"
done

# MOC coverage: % of notes appearing in at least one MOC's Core Ideas
COVERED=0
for f in "$NOTES_DIR"/*.md; do
  NAME=$(basename "$f" .md)
  # Skip MOCs themselves
  grep -q '^type: moc' "$f" 2>/dev/null && continue
  # Check if any MOC links to this note
  if grep -rl '^type: moc' "$NOTES_DIR"/*.md 2>/dev/null | xargs grep -l "\[\[$NAME\]\]" >/dev/null 2>&1; then
    COVERED=$((COVERED + 1))
  fi
done
echo "Coverage: $COVERED / $NOTE_COUNT"

--=={ graph health }==--

  {vocabulary.note_plural}: [N] (plus [M] {vocabulary.topic_map_plural})
  Connections: [N] (avg [X] per {vocabulary.note})
  Graph density: [0.XX]
  {vocabulary.topic_map} coverage: [N]% of {vocabulary.note_plural} appear in at least one {vocabulary.topic_map}

  Orphans ([N]):
    - [[orphan name]] — [description from YAML]
    → Suggestion: Run /{vocabulary.cmd_reflect} to find connections

  Dangling Links ([N]):
    - [[missing name]] — referenced from [[source note]]
    → Suggestion: Create the {vocabulary.note} or remove the link

  {vocabulary.topic_map} Sizes:
    - [[moc name]]: [N] {vocabulary.note_plural} [OK | WARN: approaching split threshold | WARN: consider merging]

  Overall: [HEALTHY | NEEDS ATTENTION | FRAGMENTED]

# For each note, extract outgoing wiki links
for f in "$NOTES_DIR"/*.md; do
  NAME=$(basename "$f" .md)
  LINKS=$(grep -oP '\[\[([^\]]+)\]\]' "$f" 2>/dev/null | sed 's/\[\[//;s/\]\]//' | sort -u)
  echo "FROM:$NAME"
  echo "$LINKS" | while read -r target; do
    [[ -n "$target" ]] && echo "  TO:$target"
  done
done

--=={ graph triangles }==--

  Found [N] synthesis opportunities — pairs of {vocabulary.note_plural} that share
  a common reference but do not reference each other:

  1. [[note B]] and [[note C]]
     Common parent: [[note A]]
     B: "[description]"
     C: "[description]"
     → These may benefit from a connection because [specific reasoning
        about WHY B and C might relate through A's lens]
     → Action: Run /{vocabulary.cmd_reflect} on [[note B]] to evaluate

  2. [[note D]] and [[note E]]
     Common parent: [[note F]]
     ...

  [Show top 10. If more exist: "[N] more triangles found. Show all? (yes/no)"]

--=={ graph bridges }==--

  Found [N] bridge {vocabulary.note_plural} — structurally critical nodes whose
  removal would disconnect graph regions:

  1. [[bridge note]] — connects [N] {vocabulary.note_plural} on one side to [M] on the other
     Description: "[description]"
     Cluster A: [[note1]], [[note2]], ...
     Cluster B: [[note3]], [[note4]], ...
     → Risk: If this {vocabulary.note} becomes stale, [N+M] {vocabulary.note_plural}
       lose their connection path
     → Action: Consider adding parallel connections between the clusters

  [If no bridges: "No bridge notes found. The graph has redundant paths between
   all connected regions. This is healthy."]

--=={ graph clusters }==--

  Found [N] connected components:

  Cluster 1: [size] {vocabulary.note_plural}
    Key nodes: [[note1]] (8 links), [[note2]] (6 links)
    Topics: [[topic A]], [[topic B]]
    Cross-cluster links: [N]
    → This cluster is [well-connected | isolated | a hub]

  Cluster 2: [size] {vocabulary.note_plural}
    ...

  Isolated {vocabulary.note_plural} ([N]):
    - [[isolated note]] — [description]
    → Action: Run /{vocabulary.cmd_reflect} to find connections

  [If 1 cluster: "All {vocabulary.note_plural} are in one connected component.
   The graph is fully connected. This is healthy."]

# Authority score: incoming links per note
for f in "$NOTES_DIR"/*.md; do
  NAME=$(basename "$f" .md)
  INCOMING=$(grep -rl "\[\[$NAME\]\]" "$NOTES_DIR"/ 2>/dev/null | grep -v "$f" | wc -l | tr -d ' ')
  echo "AUTH:$INCOMING:$NAME"
done | sort -t: -k2 -rn | head -10

# Hub score: outgoing links per note
for f in "$NOTES_DIR"/*.md; do
  NAME=$(basename "$f" .md)
  OUTGOING=$(grep -oP '\[\[[^\]]+\]\]' "$f" 2>/dev/null | wc -l | tr -d ' ')
  echo "HUB:$OUTGOING:$NAME"
done | sort -t: -k2 -rn | head -10

--=={ graph hubs }==--

  Top Authorities (most-linked-to):
    1. [[note]] — [N] incoming links — "[description]"
    2. [[note]] — [N] incoming links — "[description]"
    ...

  Top Hubs (most-linking-from):
    1. [[note]] — [N] outgoing links — "[description]"
    2. [[note]] — [N] outgoing links — "[description]"
    ...

  Synthesizers (high on both — structurally important):
    1. [[note]] — [N] in / [M] out — "[description]"
    ...

  [If no clear synthesizers: "No notes score high on both metrics.
   This suggests the graph has separate input and output layers."]

--=={ graph siblings: [[topic]] }==--

  {vocabulary.topic_map} [[topic]] has [N] {vocabulary.note_plural}.
  Found [M] unconnected sibling pairs:

  Likely connections:
    1. [[note A]] and [[note B]]
       A: "[description]"
       B: "[description]"
       → [Why these likely relate]

  Possible connections:
    2. [[note C]] and [[note D]]
       ...

  Appropriately separate: [N] pairs — no connection needed

  → Action: Run /{vocabulary.cmd_reflect} on the "likely" pairs

--=={ forward traversal: [[note]] (depth [N]) }==--

  [[root note]] — "[description]"
    ├── [[link 1]] — "[description]"
    │   ├── [[link 1a]] — "[description]"
    │   └── [[link 1b]] — "[description]"
    ├── [[link 2]] — "[description]"
    │   └── [[link 2a]] — "[description]"
    └── [[link 3]] — "[description]"

  Reached [N] {vocabulary.note_plural} in [depth] hops.
  Dead ends (no outgoing links): [[note X]], [[note Y]]
  Cycles detected: [[note]] → ... → [[note]] (skipped)