Preserve

/bedrock:preserve — Single Write Point for the Vault

Plugin Paths

Entity definitions and templates are in the plugin directory, not in the vault root. Use the "Base directory for this skill" provided at invocation to resolve paths:

• Entity definitions: <base_dir>/../../entities/
• Templates: <base_dir>/../../templates/{type}/_template.md
• Plugin CLAUDE.md: <base_dir>/../../CLAUDE.md (already injected automatically into context)

Where <base_dir> is the path provided in "Base directory for this skill".

Vault Resolution

Resolve which vault to operate on. This skill can be invoked from any directory.

Step 1 — Parse --vault flag: Check if the input arguments include --vault <name>. If found, extract the vault name and remove it from the arguments before further parsing.

Step 2 — Resolve vault path:

1. If --vault <name> was provided: Read the vault registry at <base_dir>/../../vaults.json. Find the entry matching the name. If not found: error — "Vault <name> is not registered. Run /bedrock:vaults to see available vaults." If found: set VAULT_PATH to the entry's path value.

2. If no --vault flag — CWD detection: Read <base_dir>/../../vaults.json. Check if the current working directory is inside any registered vault path (CWD starts with a registered vault's absolute path). If multiple match, use the longest path (most specific). If found: set VAULT_PATH to the matching vault's path.

3. If CWD detection fails — default vault: From the registry, find the vault with "default": true. If found: set VAULT_PATH to the default vault's path.

4. If no resolution: Error — "No vault resolved. Available vaults:" followed by the registry listing. "Use --vault <name> to specify, or run /bedrock:setup to register a vault."

Step 3 — Validate vault path:

test -d "<VAULT_PATH>" && echo "exists" || echo "missing"

If missing: error — "Vault path <VAULT_PATH> does not exist on disk. Run /bedrock:setup to re-register."

Step 4 — Read vault config:

cat <VAULT_PATH>/.bedrock/config.json 2>/dev/null

Extract language, git.strategy, and other relevant fields for use in later phases.

From this point forward, ALL vault file operations use <VAULT_PATH> as the root.

• Entity directories: <VAULT_PATH>/actors/, <VAULT_PATH>/people/, etc.
• Vault config: <VAULT_PATH>/.bedrock/config.json
• Git operations: git -C <VAULT_PATH> <command>

Overview

This skill centralizes ALL write logic for the vault. It receives input (structured, free-form, or graphify output), identifies entities, correlates with the existing vault, proposes changes to the user, and executes after confirmation. It is the only path to create or update entities in the vault (except /sync-people which handles people/teams via GitHub API).

You are an execution agent. Follow the phases below in order, without skipping steps.

Phase 0 — Pre-Write Setup

Two pre-flight steps run before any input parsing: synchronize the vault with its remote, then (when applicable) merge an incoming graphify output directory into the vault's cumulative graphify-out/.

0.1 Vault Sync

Execute:

git -C <VAULT_PATH> pull --rebase origin main

If the pull fails:

• No remote configured: warn "No remote configured. Working locally." and proceed.
• Pull conflict: git -C <VAULT_PATH> rebase --abort and warn the user. DO NOT proceed without resolving.
• Otherwise: proceed.

0.2 Merge Incoming Graphify Output

When this runs: Only when the skill was invoked with a graphify_output_path argument pointing at a graphify output directory (e.g., /bedrock:learn passes $TEACH_TMP/graphify-out-new/). Free-form text input and structured entity-list input skip this sub-phase entirely.

Skip condition (backward compat): If the input's graphify_output_path resolves to the same absolute path as <VAULT_PATH>/graphify-out/, skip this sub-phase. Legacy callers (and /bedrock:sync in its current form) point at the vault's own output directory — there is nothing to merge. Use realpath (or equivalent) to compare:

incoming_real=$(cd "<graphify_output_path>" 2>/dev/null && pwd -P)
vault_real=$(cd "<VAULT_PATH>/graphify-out" 2>/dev/null && pwd -P)
if [ "$incoming_real" = "$vault_real" ]; then
  echo "Phase 0.2: graphify_output_path already points at the vault — skipping merge."
  # proceed to Phase 1 with graphify_output_path unchanged
fi

Skip condition (no graphify input): If the input is free-form text, structured entity list, or otherwise does not include graphify_output_path, skip.

Step 1 — Validate incoming directory. Verify that <graphify_output_path>/graph.json exists, is non-empty, and parses as valid JSON. If invalid, abort with a clear error and do NOT mutate the vault:

if [ ! -s "<graphify_output_path>/graph.json" ]; then
  echo "ERROR: graph.json missing or empty in <graphify_output_path>. Aborting before vault mutation."
  exit 1
fi
python3 -c "import json,sys; json.load(open('<graphify_output_path>/graph.json'))" || { echo "ERROR: graph.json is not valid JSON."; exit 1; }

Step 2 — First-ingestion edge case. If <VAULT_PATH>/graphify-out/ does not exist, promote the incoming directory wholesale (no re-merge pass) and record stats, then skip to Step 7:

if [ ! -d "<VAULT_PATH>/graphify-out" ]; then
  mkdir -p "<VAULT_PATH>"
  cp -R "<graphify_output_path>" "<VAULT_PATH>/graphify-out"
  echo "Phase 0.2: first ingestion — promoted incoming graphify output to <VAULT_PATH>/graphify-out/."
  # record: nodes_added = <count of nodes in graph.json>, nodes_merged = 0, edges_added = <count of edges>, stale_flag_set = false
  # skip to Step 7 (record stats) then exit sub-phase
fi

Step 3 — Merge graph.json (nodes + edges). Both files follow NetworkX node-link format ({"nodes": [...], "edges": [...]} or "links" — accept either key). Run the merge via an inline Python block to avoid hand-merging JSON in the prompt. Write the merged graph to a staging file, then atomically swap:

python3 - <<'PY'
import json, os, pathlib, shutil, sys

existing_path = pathlib.Path("<VAULT_PATH>/graphify-out/graph.json")
incoming_path = pathlib.Path("<graphify_output_path>/graph.json")
staging_path = existing_path.with_suffix(".json.staging")

with existing_path.open() as f:
    existing = json.load(f)
with incoming_path.open() as f:
    incoming = json.load(f)

# Accept both "edges" and "links" keys — normalize to "edges".
def _edges(g):
    return g.get("edges", g.get("links", []))

# --- Node merge keyed by id ---
def _union(a, b):
    # Preserve order; dedup by string representation.
    seen, out = set(), []
    for item in (a or []) + (b or []):
        key = json.dumps(item, sort_keys=True) if not isinstance(item, str) else item
        if key not in seen:
            seen.add(key)
            out.append(item)
    return out

def _dedup_sources_by_url(a, b):
    seen, out = set(), []
    for item in (a or []) + (b or []):
        if isinstance(item, dict) and "url" in item:
            if item["url"] in seen:
                continue
            seen.add(item["url"])
        out.append(item)
    return out

existing_nodes = {n["id"]: n for n in existing.get("nodes", [])}
nodes_added = 0
nodes_merged = 0
for inc in incoming.get("nodes", []):
    nid = inc["id"]
    if nid not in existing_nodes:
        existing_nodes[nid] = inc
        nodes_added += 1
    else:
        cur = existing_nodes[nid]
        # Union sources by URL
        if "sources" in inc or "sources" in cur:
            cur["sources"] = _dedup_sources_by_url(cur.get("sources"), inc.get("sources"))
        # Most-recent updated_at (YYYY-MM-DD lexical compare works)
        cur_ua, inc_ua = cur.get("updated_at"), inc.get("updated_at")
        if inc_ua and (not cur_ua or inc_ua > cur_ua):
            cur["updated_at"] = inc_ua
        # Union labels and tags
        for key in ("labels", "tags"):
            if key in inc or key in cur:
                cur[key] = _union(cur.get(key), inc.get(key))
        nodes_merged += 1

# --- Edge dedup keyed by (source, target, type/relation) ---
def _edge_key(e):
    return (e.get("source"), e.get("target"), e.get("type") or e.get("relation"))

existing_edges = _edges(existing)
seen_edges = {_edge_key(e) for e in existing_edges}
edges_added = 0
for inc_edge in _edges(incoming):
    k = _edge_key(inc_edge)
    if k in seen_edges:
        continue
    existing_edges.append(inc_edge)
    seen_edges.add(k)
    edges_added += 1

merged = dict(existing)
merged["nodes"] = list(existing_nodes.values())
# Preserve the key naming the existing file used.
merged_key = "edges" if "edges" in existing else ("links" if "links" in existing else "edges")
merged[merged_key] = existing_edges

with staging_path.open("w") as f:
    json.dump(merged, f, indent=2, ensure_ascii=False)

# Emit stats to stdout for capture.
print(json.dumps({"nodes_added": nodes_added, "nodes_merged": nodes_merged, "edges_added": edges_added}))
PY

Atomic swap after the Python block succeeds:

mv "<VAULT_PATH>/graphify-out/graph.json.staging" "<VAULT_PATH>/graphify-out/graph.json"

If the Python block exits non-zero, abort without running the mv — the vault's graph.json stays untouched.

Step 4 — Append obsidian/*.md files. For each markdown file in <graphify_output_path>/obsidian/:

• Skip any file whose source_file frontmatter value starts with /tmp/ — these are ephemeral visualization files produced by /bedrock:teach and must not accumulate in the vault.
• If the corresponding file exists in <VAULT_PATH>/graphify-out/obsidian/: append the incoming content to the existing file, separated by \n\n---\n\n. Existing content is preserved verbatim.
• If it does not exist: copy the file into <VAULT_PATH>/graphify-out/obsidian/.

mkdir -p "<VAULT_PATH>/graphify-out/obsidian"
for src in "<graphify_output_path>/obsidian/"*.md; do
  [ -e "$src" ] || continue
  SRC_FILE=$(awk -F'"' '/^source_file:/{print $2; exit}' "$src")
  case "$SRC_FILE" in /tmp/*) continue ;; esac
  dest="<VAULT_PATH>/graphify-out/obsidian/$(basename "$src")"
  if [ -e "$dest" ]; then
    printf '\n\n---\n\n' >> "$dest"
    cat "$src" >> "$dest"
  else
    cp "$src" "$dest"
  fi
done

Step 5 — Append GRAPH_REPORT.md. If <graphify_output_path>/GRAPH_REPORT.md exists:

• If <VAULT_PATH>/graphify-out/GRAPH_REPORT.md exists: append a new dated section.
• If it does not exist: copy.

if [ -f "<graphify_output_path>/GRAPH_REPORT.md" ]; then
  dest="<VAULT_PATH>/graphify-out/GRAPH_REPORT.md"
  if [ -e "$dest" ]; then
    {
      printf '\n\n---\n\n# Merge on %s\n\n' "$(date +%Y-%m-%d)"
      cat "<graphify_output_path>/GRAPH_REPORT.md"
    } >> "$dest"
  else
    cp "<graphify_output_path>/GRAPH_REPORT.md" "$dest"
  fi
fi

Step 6 — Mark .graphify_analysis.json stale. If <VAULT_PATH>/graphify-out/.graphify_analysis.json exists, set a top-level "stale": true field. Other content is untouched:

analysis="<VAULT_PATH>/graphify-out/.graphify_analysis.json"
stale_flag_set=false
if [ -f "$analysis" ]; then
  python3 - <<PY
import json, pathlib
p = pathlib.Path("$analysis")
with p.open() as f:
    data = json.load(f)
data["stale"] = True
with p.open("w") as f:
    json.dump(data, f, indent=2, ensure_ascii=False)
PY
  stale_flag_set=true
fi

If the file does not exist, skip (nothing to mark).

Step 7 — Record merge stats for the Phase 7 report. Capture nodes_added, nodes_merged, edges_added (from Step 3's Python stdout) and stale_flag_set (from Step 6). These values are threaded through to Phase 7's report block under a new "Graphify merge" section and returned in the skill's result payload to the caller (e.g., /bedrock:learn).

Step 8 — Point subsequent phases at the merged location. After the merge succeeds, set graphify_output_path := <VAULT_PATH>/graphify-out/ for all downstream phases. Phase 1.3 (graphify-output parsing), Phase 2 (matching), and the rest of the flow read from the merged vault location — not from the original temp input.

Phase 1 — Parse Input

/bedrock:preserve accepts three input modes. Determine which to apply:

1.1 Structured input

When called by another skill (e.g., /bedrock:learn) or when the user provides an explicit list. The format is an optional top-level header followed by a list of entities:

# Optional top-level header — applies to all entities in the batch
actor_context: <actor-name>  # optional, kebab-case slug of an actor in the vault.
                             # When present, /preserve treats the batch as scoped to that actor:
                             # graphify nodes of file_type=document/paper become `code` of this actor
                             # with node_type ∈ {concept, decision} (see Phase 1.3 step 4).

entities:
  - type: actor | person | team | concept | topic | discussion | project | fleeting | code
    name: "canonical entity name"
    action: create | update
    content: "content to include in the entity body"
    relations:
      actors: ["actor-slug-1", "actor-slug-2"]
      people: ["person-slug-1"]
      teams: ["team-slug-1"]
      concepts: ["concept-slug-1"]
      topics: ["topic-slug-1"]
      discussions: ["discussion-slug-1"]
      projects: ["project-slug-1"]
      code: ["node-slug-1"]
    source: "github | confluence | jira | session | manual | gdoc | csv | graphify"
    metadata: {}  # additional frontmatter fields specific to the type

If the input is a bare list (no entities: key, no actor_context), accept it as a list of entities with actor_context = null. This preserves backward compatibility with callers that pre-date the field.

If the input follows this format (or something close): parse directly and go to Phase 2.

1.2 Free-form input

When the user provides natural text, meeting notes, session context, or any unstructured content. Analyze the text and extract:

1. Mentioned entities — identify by name, alias, or reference:

   • People: names in "First Last" format
   • Actors: service names, APIs, repositories
   • Teams: squad names
   • Concepts: patterns, principles, techniques, protocols, abstractions
   • Topics: discussion themes, bugs, RFCs, features
   • Discussions: meetings, decisions, debates
   • Projects: initiatives, migrations, cross-team features

2. Inferred action — for each entity:

   • If the entity already exists in the vault: update
   • If the entity does not exist: create

3. Content — what was said about each entity in the input

4. Relations — infer which entities relate to each other based on context

5. Source — infer: session (conversation), meeting-notes (minutes), manual (typed text)

To classify new content, consult the plugin's entity definitions (see "Plugin Paths" section) (loaded in Phase 2.0):

• "When to create" section → positive criteria for creating a new entity
• "When NOT to create" section → exclusion criteria
• "How to distinguish from other types" section → disambiguation

Convert the result to the structured format from section 1.1 and proceed.

1.3 Graphify output input

When called by /bedrock:learn (or any skill) with a graphify output reference, OR when the user invokes /bedrock:preserve directly pointing at a graphify-out/ directory:

Input format:

• graphify_output_path: path to graphify-out/ directory
• source_url: original external source URL/path (optional — may not be present for manual invocation)
• source_type: type of external source (optional)
• actor_context: kebab-case slug of an actor in the vault (optional). When present, the entire corpus is treated as belonging to that actor: file_type=document/paper nodes are classified as code of that actor with node_type ∈ {concept, decision} instead of as global concept/topic/fleeting. When absent, classification falls back to the corpus-agnostic logic (concept global / topic / fleeting).

Detection: If the input contains a path ending in graphify-out/ or graphify-out, or references graph.json, treat as graphify output input.

Processing:

1. Read graph.json from graphify_output_path/graph.json:

   • Parse NetworkX node-link format
   • Extract all nodes with: id, label, file_type, source_file, source_location
   • Extract all edges with: source, target, relation, confidence, confidence_score
   • If graph.json is missing or empty: abort with error "No graph.json found in graphify output. Run /graphify first."

2. Read obsidian files from graphify_output_path/obsidian/*.md:

   • For each markdown file, read frontmatter and body content
   • Correlate with graph.json by matching filename stem to node id (kebab-cased)
   • If obsidian file doesn't exist for a node: fall back to graph.json metadata alone

3. Read analysis from graphify_output_path/.graphify_analysis.json (if exists):

   • Extract community assignments (community_id per node), god nodes (is_god_node), community labels
   • Use community labels to inform domain/* tags when creating entities
   • If absent or stale: true, downstream steps fall back to graph-only signals (no community-aware grouping)

4. Read configuration from <VAULT_PATH>/.bedrock/config.json (best-effort):

   • code.max_per_actor: integer, default 200. Per-actor cap on the number of code candidates produced from this corpus. No absolute global cap.
   • code.cluster_threshold: float, default 0.85. Minimum semantically_similar_to.confidence_score for two nodes to be grouped into the same code candidate.
   • If .bedrock/config.json is missing or has no code block, use the defaults silently.

5. Group nodes by semantic similarity (BEFORE filtering and classification) — produces clusters that will each become at most one code candidate:

   • Build clusters by union-find:
     • Two nodes are in the same cluster if there is a semantically_similar_to edge between them with confidence_score ≥ code.cluster_threshold.
     • OR they share the same community_id (from .graphify_analysis.json) AND at least one of them is is_god_node OR both have edge_count ≥ 2. This guards against weakly-tied community co-membership.
   • If .graphify_analysis.json is absent or stale, only the semantically_similar_to rule applies.
   • Singletons (nodes with no qualifying neighbor) form their own cluster of size 1.
   • Each cluster carries: cluster_id (synthetic), member_node_ids[] (the union of node ids — this becomes the graphify_node_ids array of the resulting code entity), representative (the node with highest degree in the cluster — used for label, source_file, etc.).
   • Hard cap: maximum 50 nodes per cluster (defensive — runaway clusters indicate bad threshold).

6. Classify clusters into vault entity types — /preserve owns this classification. Read ALL entity definitions from the plugin (see "Plugin Paths") and apply:

   When actor_context is present (single-actor corpus):

   • file_type: code clusters → code for the actor, node_type ∈ {function, class, module, interface, endpoint} inferred from the representative node's label/edges.
   • file_type: document or file_type: paper clusters → code for the actor:
     • node_type: decision if the representative node has rationale_for edges OR the label/text contains decision markers (e.g., "ADR", "RFC", "decision", "chose", "decided").
     • node_type: concept otherwise.
   • The cluster's actor field is set to [[<actor_context>]] for all entities.

   When actor_context is absent (corpus-agnostic):

   • file_type: code clusters → code (parent actor inferred from source_file path or repo name in the path; if no actor can be inferred, classify as fleeting).
   • file_type: document or file_type: paper clusters → check for concept first: if the representative node describes a pattern, principle, technique, protocol, or abstraction AND is self-contained AND is not specific to a single actor → concept (global).
     • Non-concept document → classify using entity definitions ("When to create" / "When NOT to create" / "How to distinguish").
     • Non-concept paper → topic or fleeting depending on completeness criteria.
   • God nodes (is_god_node) → consider as actor, concept, or topic.
   • Apply Zettelkasten classification (section 1.4): if content doesn't meet completeness criteria → fleeting.

7. Filter relevant clusters (applied to code candidates only — non-code classifications keep their existing inclusion logic):

   • Inclusion predicate: representative node's strongest edge has confidence ∈ {EXTRACTED, INFERRED} AND at least one of:
     • is_god_node (from .graphify_analysis.json),
     • degree > community_average_degree (from .graphify_analysis.json; if analysis absent, use overall graph average),
     • edge_count ≥ 2.
   • Exclusion: representative label matches trivial patterns (case-insensitive substring of Test, Tests, Mock, Fake, Builder, Stub, Fixture) or the cluster only contains nodes flagged trivial by graphify.
   • Per-actor cap: group surviving code candidates by their resolved actor. Within each actor, rank by is_god_node (true first) > degree > edge_count. Keep the top code.max_per_actor (default 200); discard the rest with a warning in the report listing how many were dropped per actor.
   • No English keyword regex. The previous label allowlist (Service|Controller|...) is removed.
   • For non-code classifications (concept global, topic, fleeting): include all that pass classification.

8. Match against existing vault — Use the textual matching logic from Phase 2 (filename, name, aliases, graphify ids). For code entities, the graphify-id match accepts both legacy singular graphify_node_id and the new graphify_node_ids array — match if the cluster's member_node_ids set intersects the entity's existing id set. Mark matched clusters as update, unmatched as create.

9. Build internal structured format for each classified + filtered cluster:

   • type: from classification (step 6).
   • name: kebab-cased label of the cluster's representative node.
   • action: create or update (from step 8 matching).
   • content: body of the obsidian markdown file matching the representative's id (or generate from graph.json metadata if no obsidian file). When the cluster has multiple members, include a brief "Grouped from N graphify nodes" note in the body listing the member ids — this preserves traceability.
   • relations: from graph.json edges of all member nodes (convert node ids to entity slugs via kebab-case; deduplicate).
   • source: from input source_type (or "graphify" if not provided).
   • source_url: from input source_url (if provided).
   • source_type: from input source_type (if provided).
   • metadata: for code entities, include:
     • graphify_node_ids: array — the cluster's member_node_ids (always written as array even when size is 1).
     • actor: wikilink of the parent actor ([[<actor_context>]] when set; otherwise inferred).
     • node_type: from step 6.
     • source_file: relative path from the representative node.
     • confidence: strongest edge confidence across all member nodes (EXTRACTED > INFERRED > AMBIGUOUS).
   • metadata: for concept (global) entities from graphify, include:
     • graphify_node_ids: array.
     • confidence: strongest edge confidence across all members.

10. Proceed to Phase 3 (Change Proposal) — present the classified cluster list for user confirmation, then execute writes as normal (Phases 4-7).

Note: When invoked directly by the user (not via /learn), the user confirmation in Phase 3 is the only gate before writes. When invoked via /learn, /learn has already shown the user the graphify report (god nodes, communities) providing context for the confirmation.

1.4 Zettelkasten Classification

Before converting to structured format, classify each entity by Zettelkasten role. Consult the plugin's entity definitions ("Completeness Criteria" section) to determine the correct type:

Classification rule:

• If the content meets the completeness criteria of a permanent type (actor, person, team) → classify as permanent
• If the content has a non-empty graphify_node_ids array (or legacy singular graphify_node_id) and actor defined → classify as code (permanent extension, sub-entity of actor)
• If the content defines a pattern, principle, technique, protocol, or abstraction that is self-contained and actor-independent → classify as concept (permanent)
• If the content meets the completeness criteria of a bridge type (topic, discussion) → classify as bridge
• If the content meets the completeness criteria of an index type (project) → classify as index
• If the content does NOT meet the completeness criteria of any type → classify as fleeting

Heuristics for fleeting:

• Vague mention without concrete data (no repo name, no full person name, no date, no decision)
• Idea or hypothesis without confirmation ("it seems like...", "maybe...", "someone mentioned...")
• Fragment of information without sufficient context to be self-contained
• Generic TODO without assignee or deadline

When in doubt, err on the side of fleeting — it is safer to capture as fleeting and promote later than to create an incomplete permanent entity.

If the input came from another skill (e.g., /bedrock:learn) and already includes a classification suggestion (type: fleeting), respect the suggestion but validate against the criteria above.

If no input was provided: ask the user "What would you like to preserve in the vault? Provide text, meeting notes, or a list of entities."

Phase 2 — Matching with Existing Entities

Objective: Correlate entities from the input with the existing vault.

2.0 Read entity definitions

Read ALL entity definition files from the plugin (see "Plugin Paths" section): <base_dir>/../../entities/*.md These files define what each entity type is, when to create, when NOT to create, and how to distinguish between types. Internalize these definitions — you will use them to classify new content (especially in free-form mode, Phase 1.2).

2.1 Collect vault entities

List all files in each entity directory (exclude _template.md and _template_node.md):

<VAULT_PATH>/actors/*.md and <VAULT_PATH>/actors/*/*.md (actors can be folders)
<VAULT_PATH>/actors/*/nodes/*.md (code entities within actors)
<VAULT_PATH>/people/*.md
<VAULT_PATH>/teams/*.md
<VAULT_PATH>/topics/*.md
<VAULT_PATH>/discussions/*.md (if exists)
<VAULT_PATH>/projects/*.md (if exists)
<VAULT_PATH>/fleeting/*.md (if exists)

For each file found, extract:

• filename (without extension) — canonical identifier
• name (or title) from frontmatter — human-readable name
• aliases from frontmatter — alternative names
• graphify_node_ids from frontmatter — for code entities (if present, accept both the new array form and the legacy singular graphify_node_id string; normalize to a set of ids per entity)

2.2 Textual matching

For each entity from the input, check if it already exists in the vault:

Match rules (in priority order):

1. Exact match by filename (case-insensitive): billing-api == billing-api
2. Match by name/title field (case-insensitive): "Billing API" finds billing-api.md
3. Match by aliases (case-insensitive): "BillingAPI" finds billing-api.md if alias contains "BillingAPI"
4. Match by filename without hyphens (case-insensitive): billing-api → billingapi finds "BillingAPI"
5. Match by graphify ids (for code entities): set intersection between the input cluster's graphify_node_ids (array) and the vault entity's id set, where the vault entity's id set is normalized from EITHER graphify_node_ids (array, current schema) OR the legacy singular graphify_node_id (string treated as a 1-element set). Any non-empty intersection is a match. This is the most reliable match for code entities and takes priority over the others when present.

Safety rules:

• DO NOT match by substrings of 3 characters or fewer (e.g., "api" should not match everything)
• Maximum 20 correlations per entity type
• In case of ambiguity: record all candidates and resolve in Phase 3 (proposal)

2.3 Classify actions

For each entity from the input:

• If match found in vault: mark as update (update existing entity)
• If no match: mark as create (new entity)
• If the input already specified the action: respect the input's action

2.4 Enrich via external sources (best-effort)

For entities of type actor that have a repository field in frontmatter:

GitHub MCP (call directly, NOT via subagent):

• mcp__plugin_github_github__list_pull_requests → recent PRs (5, state=all, sort=updated)
• mcp__plugin_github_github__list_commits → recent commits (5)

Atlassian MCP:

• Search for Jira issues from the relevant squad
• Search for related Confluence pages

IMPORTANT: Enrichment is best-effort. If MCP is not available or fails, continue without it. Record which sources failed in the final report.

IMPORTANT: DO NOT use subagents for MCP calls. Permissions are not inherited by subagents.

Phase 3 — Change Proposal

Objective: Present to the user EVERYTHING that will be done, BEFORE executing.

3.1 Build proposal

For each entity, present:

## Change Proposal — /bedrock:preserve

### Entities to create
| # | Type | Name | File | Relations |
|---|---|---|---|---|
| 1 | actor | billing-new-api | actors/billing-new-api.md | [[squad-payments]], [[alice-smith]] |

### Entities to update
| # | Type | Name | File | Changes |
|---|---|---|---|---|
| 1 | actor | billing-api | actors/billing-api.md | Add "Recent Activity" section |

### Bidirectional links
| Source entity | Target entity | Section added |
|---|---|---|
| [[billing-new-api]] | [[squad-payments]] | "Related Actors" in squad-payments |
| [[squad-payments]] | [[billing-new-api]] | "team" in billing-new-api |

### Sources consulted
- ✅ Local vault
- ✅ / ❌ GitHub MCP
- ✅ / ❌ Atlassian MCP

Total: N entities to create, M to update, P bidirectional links.

3.2 Await confirmation

Ask: "Confirm execution? (yes/no/adjust)"

• yes: proceed to Phase 4
• no: abort and inform
• adjust: ask what to adjust, modify proposal, re-present

DO NOT proceed without explicit user confirmation.

Phase 4 — Execute Changes

Objective: Create and update entities as per the approved proposal.

4.1 Create new entities

For each entity marked as create:

1. Read the plugin template: <base_dir>/../../templates/<directory>/_template.md
2. Fill frontmatter with data from input + matching:
   • type: entity type
   • name (or title for topics): extracted name
   • aliases: generate at least 1 alias following the convention per type (see conventions.md)
   • tags: use hierarchical tags: [type/<type>, status/<status>, domain/<domain>]
   • updated_at: today's date (YYYY-MM-DD)
   • updated_by: "preserve@agent"
   • Relation fields: wikilinks to correlated entities
   • Remaining fields: fill with data from input or leave empty
3. Fill body following the template structure
4. Add mandatory callouts when applicable:
   • Actors with status: deprecated → > [!warning] Deprecated
   • Actors with pci: true → > [!danger] PCI Scope
5. Save to <directory>/<filename>.md

Rules per entity type:

4.1.2 Code entity specific rules

When creating a code entity:

1. Resolve the parent actor: the actor field in the input (wikilink or slug) indicates the actor. Verify that the actor exists in actors/.
2. Ensure folder structure: if the actor is still a flat file (actors/<name>.md):
   • Create folder actors/<name>/
   • Move actors/<name>.md → actors/<name>/<name>.md (use git mv)
   • Create subfolder actors/<name>/nodes/
   • Add "Knowledge Nodes" section to the actor body (before the "Infrastructure" section or at the end)
3. Create code entity: use template actors/_template_node.md
   • Save to actors/<actor>/nodes/<node-slug>.md
   • Filename: kebab-case of the node's name (e.g., ProcessTransaction → process-transaction.md)
   • Fill graphify_node_ids (array — always written as a list, even of size 1), actor, node_type, source_file, confidence from the input
   • Backward compat at write time: if the input still carries the legacy singular graphify_node_id (string), normalize it to graphify_node_ids: [<id>] before writing. Never persist the singular form.
   • Inherit domain/* tags from the parent actor
   • Generate at least 1 alias (human-readable name + camelCase if applicable)
4. Bidirectional backlink:
   • In the code entity: actor: "[[actor-name]]" in frontmatter
   • In the actor: add - [[node-slug]] — brief description in the "Knowledge Nodes" section

4.1.1 Linking rules by Zettelkasten role

When filling the entity body, apply semantic linking rules by role:

• Permanent notes (actors, people, teams, concepts): wikilinks in the body must have textual context. E.g., "receives authorizations from [[payment-gateway]] via gRPC" — not just "[[payment-gateway]]"
• Bridge notes (topics, discussions): wikilinks in the body explain why permanents relate. E.g., "the deprecation of [[legacy-gateway]] is blocked because clients depend on [[billing-api]]"
• Index notes (projects): wikilinks in the body point to where the knowledge is. E.g., "progress documented in [[2026-06-deprecation-legacy-gateway]]"
• Fleeting notes: exploratory wikilinks allowed without full textual context.

4.2 Update existing entities

For each entity marked as update:

1. Read the existing file
2. Frontmatter: merge — update fields with new data. NEVER delete existing fields.
   • ALWAYS update updated_at and updated_by
   • Add new wikilinks to existing arrays (do not duplicate)
   • Add new aliases if discovered
3. Body:
   • Actors: can be modified/merged — new information replaces outdated information
   • People, Teams, Concepts, Topics: append-only — add information, NEVER delete existing content
   • Discussions, Projects: append-only for the general body; structured fields (action_items, conclusions) can be updated
   • "Recent Activity" section (actors): REPLACE content (temporal data)
4. Wikilinks: add new ones, NEVER remove existing ones

4.3 Populate sources field (when applicable)

If the input contains source_url and source_type (provided by /bedrock:learn or another caller):

When creating an entity:

• Add to frontmatter:

  sources:
    - url: "<source_url>"
      type: "<source_type>"
      synced_at: "<today's date>"
  

When updating an entity:

1. Read the existing sources field from frontmatter
2. If the URL already exists in the list: update synced_at with today's date
3. If the URL does not exist: append new entry {url, type, synced_at}
4. Sort by synced_at descending (most recent first)
5. NEVER remove existing entries (append-only)

If the input does NOT contain source_url: do not modify the sources field — keep the existing value (or [] if new entity).

Phase 5 — Bidirectional Linking

Objective: Ensure that every relation is reciprocal.

5.1 Linking rules

When creating/updating entity X with a reference to entity Y:

• Check if Y already references X
• If NOT: add reference from Y → X

Bidirectional linking graph:

Team ──members──→ Person ──team──→ Team
Team ──actors──→ Actor ──team──→ Team
Topic ──people──→ Person
Topic ──actors──→ Actor
Person ──focal_points──→ Actor
Project ──focal_points──→ Person ──projects──→ Project
Project ──related_actors──→ Actor
Project ──related_topics──→ Topic
Project ──related_teams──→ Team
Discussion ──related_actors──→ Actor
Discussion ──related_people──→ Person
Discussion ──related_projects──→ Project
Discussion ──related_topics──→ Topic
Code ──actor──→ Actor ──"Knowledge Nodes" section──→ Code
Code ──relations──→ Code (bidirectional via relations[])

5.2 Implementation

For each pair (X → Y) in the approved proposal:

1. Read entity Y
2. Identify the corresponding field/section in the reverse link (Y → X)
3. In frontmatter: if the array field exists, add wikilink [[X]] if not already present
4. In body: if there is a corresponding section (e.g., ## Discussions, ## Related Projects):
   • If section exists: add - [[X]] — brief context at the end of the list
   • If section does NOT exist: create the section in the appropriate location (before "Expected Bidirectional Links" or before the last ---)
5. Update updated_at and updated_by of Y
6. Save

Idempotency: if the wikilink [[X]] already exists in Y's field/section, DO NOT add it again.

5.3 Linking sections by target entity type

For frontmatter-based links (team↔actor, team↔person, person↔team, etc.): use only the YAML field, do not create a body section.

Phase 6.5 — Sync Graph Back-Pointers

Objective: Propagate vault_entity_path to the corresponding nodes in <VAULT_PATH>/graphify-out/graph.json, closing the bidirectional bridge between each code entity touched in this run and the graphify nodes it materializes.

This phase runs AFTER bidirectional linking (Phase 5) and BEFORE the git workflow (Phase 6), so the back-pointer change lands in the same commit as the entities.

6.5.1 Defensive cleanup

Remove any orphaned staging file from a prior interrupted run before doing anything else:

rm -f "<VAULT_PATH>/graphify-out/graph.json.staging" 2>/dev/null || true

This is idempotent and never fails the phase.

6.5.2 Best-effort detection

Locate the vault's cumulative graph file:

GRAPH_PATH="<VAULT_PATH>/graphify-out/graph.json"
test -s "$GRAPH_PATH" && echo "EXISTS" || echo "MISSING"

If the path does NOT exist, OR the file is empty (-s returns false), OR JSON parsing fails:

• Record phase_6_5_status = "skipped" and phase_6_5_reason ("missing", "empty", or "invalid_json").
• Skip directly to Phase 6 — do NOT fail /preserve.
• The Phase 7 report includes a warning surface (see §6.5.6 below).

If the file exists and parses, continue.

6.5.3 Collect target node ids from touched code entities

Iterate over every entity created or updated in Phase 4 with type: code. For each one, normalize the graphify ids to a set:

ids = set(

…(truncated)