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:teach 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/:

• 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 "$src" ] || continue
  dest="<VAULT_PATH>/graphify-out/obsidian/$(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:teach).

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:teach) or when the user provides an explicit list. The format is a list of entities, each with:

- 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 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:teach (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)

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, god nodes, community labels
   • Use community labels to inform domain/* tags when creating entities

4. Classify graphify nodes into vault entity types — /preserve owns this classification:

   • Read ALL entity definitions from plugin (see "Plugin Paths")
   • For each graphify node, classify:
     • file_type: code → code (actor inferred from source_file path or repo name in the path)
     • file_type: document or file_type: paper → check for concept first: if the node describes a pattern, principle, technique, protocol, or abstraction AND is self-contained AND is not specific to a single actor → concept
     • file_type: document (non-concept) → classify using entity definitions ("When to create" / "When NOT to create" / "How to distinguish")
     • file_type: paper (non-concept) → topic or fleeting depending on completeness criteria
     • God nodes (high degree in .graphify_analysis.json) → consider as actor, concept, or topic
     • Apply Zettelkasten classification (section 1.4): if content doesn't meet completeness criteria → fleeting

5. Filter relevant nodes:

   • For code entities: select top ~50 by relevance (degree > average, or label contains "Service", "Controller", "Client", "Factory", "Handler", "Mapper", "Gateway", "Provider"). Exclude test nodes (labels with "Test", "Tests", "Builder", "Mock", "Fake") and trivial nodes (getters, setters, simple DTOs).
   • For document/paper nodes: include all.

6. Match against existing vault — Use existing textual matching logic from Phase 2 (filename, name, aliases, graphify_node_id). Mark matched nodes as update, unmatched as create.

7. Build internal structured format for each classified + filtered entity:

   • type: from classification (step 4)
   • name: from graphify node label (kebab-cased for filename)
   • action: create or update (from step 6 matching)
   • content: from obsidian markdown file body (or generate from graph.json metadata if no obsidian file)
   • relations: from graph.json edges (convert node ids to entity slugs via kebab-case)
   • 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_id: node id from graph.json
     • actor: wikilink of the parent actor (inferred from source_file path)
     • node_type: infer from context (function, class, module, interface, endpoint)
     • source_file: relative path from graph.json
     • confidence: from the strongest edge connected to the node (EXTRACTED > INFERRED > AMBIGUOUS)
   • metadata: for concepts (from graphify), include:
     • graphify_node_id: node id from graph.json
     • confidence: from the strongest edge connected to the node (EXTRACTED > INFERRED > AMBIGUOUS)

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

Note: When invoked directly by the user (not via /teach), the user confirmation in Phase 3 is the only gate before writes. When invoked via /teach, /teach 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 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:teach) 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_id from frontmatter — for code entities (if present)