compress

name	compress
description	Vault alignment engine. Detects and fixes 5 types of structural misalignments: broken backlinks, concept fragmentation, entity miscategorization, duplicated entities, and misnamed entities. Delegates all writes to /bedrock:preserve. Supports interactive mode (user confirmation) and cron mode (autonomous mechanical fixes + queued semantic proposals). Use when: "bedrock compress", "bedrock-compress", "align vault", "fix backlinks", "fix misalignments", "/bedrock:compress".
user_invocable	true
allowed-tools	Bash, Read, Glob, Grep, Skill, Agent

/bedrock:compress — Vault Alignment Engine

Plugin Paths

Entity definitions and templates are in the plugin directory, not 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 compress. 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 parsing --mode.

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. Store the resolved vault name as VAULT_NAME.

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. Store its name as VAULT_NAME.

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. Store its name as VAULT_NAME.

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.
• Git operations: git -C <VAULT_PATH> <command>
• When delegating to /bedrock:preserve, pass --vault <VAULT_NAME>

---

Overview

This skill scans all entities in the vault, detects 5 types of structural misalignments, proposes fixes to the user, and delegates all writes to /bedrock:preserve.

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

Execution modes

The skill accepts an optional --mode argument:

• interactive (default): all 5 capabilities prompt the user for confirmation before execution.
• cron: capabilities 1 and 4 (mechanical, deterministic) execute autonomously without confirmation. Capabilities 2, 3, and 5 (semantic, judgment-dependent) are detected but written as a proposal to a fleeting note for human review — they are NOT executed.

Parse the mode from the invocation arguments. If no --mode is specified, default to interactive.

Five alignment capabilities

#	Capability	Type	Cron behavior
1	Broken backlinks	Mechanical	Autonomous — fix without confirmation
2	Concept match	Semantic	Queued — write proposal to fleeting note
3	Entity misalignment	Semantic	Queued — write proposal to fleeting note
4	Duplicated entities	Mechanical	Autonomous — fix without confirmation
5	Misnamed entities	Semantic	Queued — write proposal to fleeting note

Critical rules:

• NEVER write entity files directly — all mutations go through /bedrock:preserve
• NEVER execute semantic capabilities (2, 3, 5) without confirmation in interactive mode
• NEVER execute semantic capabilities (2, 3, 5) autonomously in cron mode — always queue
• NEVER remove existing wikilinks
• NEVER delete entities (compress aligns, it does not delete)
• People/Teams/Concepts/Topics: append-only — never delete content
• Actors: free merge — may edit body freely

---

Phase 0 — Sync the Vault

Execute:

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

If it fails:

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

---

Phase 1 — Scan and Detect

Scan the entire vault and run all 5 detection algorithms. Store results for Phase 2.

1.0 Load entity definitions

Read the entity definitions from the plugin directory to understand classification criteria:

• <base_dir>/../../entities/concept.md — needed for capability 2 (concept match)
• <base_dir>/../../entities/*.md — needed for capability 3 (entity misalignment)

Store the "When to create", "When NOT to create", and "How to distinguish" sections from each entity definition for use in detection.

1.1 Read all entities

For each entity directory (<VAULT_PATH>/actors/, <VAULT_PATH>/people/, <VAULT_PATH>/teams/, <VAULT_PATH>/concepts/, <VAULT_PATH>/topics/, <VAULT_PATH>/discussions/, <VAULT_PATH>/projects/, <VAULT_PATH>/fleeting/):

1. List all .md files, excluding _template.md and _template_node.md
   • For actors: include both <VAULT_PATH>/actors/*.md (flat) and <VAULT_PATH>/actors/*/*.md (folder)
2. For each entity, read frontmatter + body
3. Extract:
   • type from frontmatter
   • name from frontmatter (or filename as fallback)
   • aliases from frontmatter (array)
   • All wikilinks [[target]] from body AND frontmatter arrays
   • All proper nouns, service names, team names, person names mentioned in the body (for capabilities 4 and 5)

Optimization for large vaults: If the vault has more than 100 entities in a type, use subagents via Agent tool to parallelize reading by entity type.

Output: vault_data map: entity_name → {type, name, aliases[], wikilinks[], body_mentions[], frontmatter, body}

1.2 Capability 1 — Detect broken backlinks

For each entity A in vault_data:

1. For each wikilink [[B]] found in A (body or frontmatter arrays):
   • Skip if B does not exist as an entity file in the vault (wikilinks to non-existent entities are valid in Obsidian)
   • If B exists: check if B contains a wikilink [[A]] (body or frontmatter arrays)
   • If B does NOT link back to A: register as broken backlink

Output: broken_backlinks[] — list of {source: A, target: B, direction: "A→B exists, B→A missing"}

1.3 Capability 2 — Detect concept fragmentation

Scan all entity bodies for recurring terms or phrases that:

1. Appear in 3+ different entities (across any types)
2. Do NOT have a corresponding entity file in <VAULT_PATH>/concepts/ (or any other entity directory)
3. Are NOT already wrapped in a wikilink [[term]]

For each candidate term, evaluate against the concept entity definition (entities/concept.md):

• Is it timeless and definitional? (not temporal, not an initiative)
• Is it actor-independent? (not specific to one system's implementation)
• Does it match "When to create" criteria?
• Does it NOT match "When NOT to create" criteria?

Filter out:

• Common English words and generic terms
• Terms that are already entity filenames or aliases
• Terms shorter than 2 words (unless they are well-known patterns like "CQRS", "mTLS")

Output: concept_candidates[] — list of {term, occurrences: [{entity, context_snippet}], meets_concept_criteria: bool}

1.4 Capability 3 — Detect entity misalignment

For each entity in vault_data:

1. Read the entity's frontmatter type field
2. Read the corresponding entity definition from entities/<type>.md
3. Evaluate the entity's content against:
   • "When to create" criteria for the current type → does the entity still qualify?
   • "When NOT to create" criteria for the current type → does the entity violate any?
   • "How to distinguish" table → does the entity look like another type?
4. If a different type is a better fit:
   • Score the entity against "When to create" criteria of the proposed new type
   • Score the entity against "When NOT to create" criteria of the proposed new type
   • If the new type scores higher: flag as misaligned

Focus on these common misalignments:

• Fleeting notes that have matured into topics, actors, or concepts (critical mass, corroboration)
• Topics that are actually concepts (timeless definition vs. temporal initiative)
• Actors that are actually projects (no repo/deployment yet)

Output: misaligned_entities[] — list of {entity, current_type, proposed_type, reason}

1.5 Capability 4 — Detect duplicated entities

Scan all entity bodies for proper nouns, service names, team names, and person names that:

1. Are mentioned in 3+ different entity files
2. Do NOT have a corresponding entity file anywhere in the vault
3. Are NOT already wrapped in a wikilink [[name]]

Identification heuristics:

• Capitalized multi-word phrases (e.g., "Payment Gateway", "Alice Smith")
• Kebab-case or camelCase terms that look like service names (e.g., "billing-api", "notificationService")
• Terms following patterns like "the X team", "the X service", "X squad"

Filter out:

• Terms that are already entity filenames or aliases (existing entities)
• Generic organizational terms ("the team", "the service", "the API")
• Terms that appear only within wikilinks (already linked)

Output: missing_entities[] — list of {name, inferred_type, mentions: [{entity, context_snippet}]}

1.6 Capability 5 — Detect misnamed entities

Scan for name variants of the same real-world entity:

1. For each entity, collect all known names: filename (kebab-case), name field, aliases[]
2. For each proper noun/service name found in body text across the vault:
   • Check if it is a variant of an existing entity name (case-insensitive, with/without hyphens, abbreviated forms)
   • Example matches: "Iury" ↔ "Iury Krieger", "billing-api" ↔ "BillingAPI" ↔ "Billing API"
3. If a mention is a variant of an existing entity but NOT wrapped in a wikilink AND the variant is NOT in the entity's aliases[]: flag as misnamed
4. If two distinct entity files refer to the same real-world entity (e.g., iury.md and iury-krieger.md): flag as duplicate entity files requiring merge

Output: misnamed_entities[] — list of {canonical_entity, variant_name, found_in: [{entity, context_snippet}], action: "add_alias" | "merge_entities"}

---

Phase 2 — Build Proposal

Present all findings to the user in a structured report, grouped by capability.

2.1 Summary table

## /bedrock:compress — Alignment Proposal

| # | Capability | Findings | Mode |
|---|---|---|---|
| 1 | Broken backlinks | N found | Autonomous / Interactive |
| 2 | Concept match | N candidates | Queued / Interactive |
| 3 | Entity misalignment | N misaligned | Queued / Interactive |
| 4 | Duplicated entities | N missing | Autonomous / Interactive |
| 5 | Misnamed entities | N variants | Queued / Interactive |

**Total findings:** N
**Mode:** interactive / cron

2.2 Capability 1 — Broken backlinks

### Capability 1: Broken Backlinks

| # | Source | Target | Missing direction |
|---|---|---|---|
| 1 | [[entity-a]] | [[entity-b]] | entity-b → entity-a |
| 2 | [[entity-c]] | [[entity-d]] | entity-d → entity-c |

**Fix:** Add missing backlinks in target entities via /bedrock:preserve.

If no broken backlinks found: "No broken backlinks found."

2.3 Capability 2 — Concept match

### Capability 2: Concept Fragmentation

| # | Candidate concept | Occurrences | Entities |
|---|---|---|---|
| 1 | "event sourcing" | 5 | [[actor-a]], [[topic-b]], [[actor-c]], ... |
| 2 | "circuit breaker" | 3 | [[actor-d]], [[actor-e]], [[topic-f]] |

**Fix:** Create concept entities and add wikilinks in referencing entities via /bedrock:preserve.

If no candidates found: "No concept fragmentation found."

2.4 Capability 3 — Entity misalignment

### Capability 3: Entity Misalignment

| # | Entity | Current type | Proposed type | Reason |
|---|---|---|---|---|
| 1 | [[note-about-cqrs]] | fleeting | concept | Meets critical mass: >3 paragraphs, timeless definition |
| 2 | [[new-checkout-system]] | actor | project | No repo or deployment yet |

**Fix:** Recategorize via /bedrock:preserve (create under new type, mark original as promoted/consolidated).

If no misalignments found: "No entity misalignments found."

2.5 Capability 4 — Duplicated entities

### Capability 4: Missing Entities (Mentioned but Not Created)

| # | Name | Inferred type | Mentions |
|---|---|---|---|
| 1 | "Payment Gateway" | actor | 4 mentions in [[topic-a]], [[actor-b]], [[discussion-c]], [[actor-d]] |
| 2 | "Alice Smith" | person | 3 mentions in [[discussion-e]], [[topic-f]], [[discussion-g]] |

**Fix:** Create missing entities and establish backlinks via /bedrock:preserve.

If no missing entities found: "No duplicated entity mentions found."

2.6 Capability 5 — Misnamed entities

### Capability 5: Misnamed Entities

| # | Canonical entity | Variant found | Found in | Action |
|---|---|---|---|---|
| 1 | [[iury-krieger]] | "Iury" | [[discussion-a]], [[topic-b]] | Add alias + wikilink |
| 2 | [[billing-api]] | "BillingAPI" | [[actor-c]] | Add alias + wikilink |
| 3 | [[iury.md]] + [[iury-krieger.md]] | Same person | — | Merge entities |

**Fix:** Add aliases and wikilinks, or merge duplicate entity files via /bedrock:preserve.

If no misnamed entities found: "No misnamed entities found."

2.7 No findings

If ALL 5 capabilities found 0 issues: Report "Vault is aligned. No misalignments detected." and end (skip Phases 3-5).

---

Phase 3 — Confirmation and Mode Handling

Interactive mode (--mode interactive or default)

Present the full proposal from Phase 2 and ask:

Confirm execution? (yes / no / partial)
- **yes**: execute all findings
- **no**: abort
- **partial**: specify which capabilities or individual findings to execute (e.g., "only capability 1 and 4", "all except finding 3 in capability 5")

STOP HERE and wait for user confirmation.

If the user says "no": report "No changes made." and end. If the user partially confirms: filter the execution list accordingly.

Cron mode (--mode cron)

No user confirmation needed for mechanical capabilities. Split findings:

Autonomous execution (capabilities 1 and 4):

• Proceed directly to Phase 4 with all findings from capabilities 1 and 4.
• When invoking /bedrock:preserve, include in the prompt: "Autonomous mode — do not ask for confirmation, process directly."

Queued proposals (capabilities 2, 3, and 5):

• If there are findings in capabilities 2, 3, or 5: compile them into a single fleeting note and delegate creation to /bedrock:preserve:

entities:
  - type: fleeting
    name: "<today's date YYYY-MM-DD>-compress-proposals"
    action: create
    content: |
      ## Compress Alignment Proposals — <today's date>

      The following alignment issues were detected by `/bedrock:compress` running in cron mode.
      Review each proposal and run `/bedrock:compress` in interactive mode to execute.

      ### Concept Fragmentation (Capability 2)
      <formatted findings from Phase 2.3>

      ### Entity Misalignment (Capability 3)
      <formatted findings from Phase 2.4>

      ### Misnamed Entities (Capability 5)
      <formatted findings from Phase 2.6>
    relations: {}
    source: "compress"
    metadata:
      status: "raw"
      source: "session"
      captured_at: "<today's date YYYY-MM-DD>"

• Include in the /bedrock:preserve invocation: "Autonomous mode — do not ask for confirmation, process directly."

---

Phase 4 — Delegate to /bedrock:preserve

4.1 Compile structured entity list

Build the entity list in the format accepted by /bedrock:preserve, grouping all confirmed fixes:

Capability 1 fixes (broken backlinks)

For each broken backlink {source: A, target: B}:

- type: <B's entity type>
  name: "<B's entity name>"
  action: update
  content: ""
  relations:
    <A's type plural>: ["<A's entity name>"]
  source: "compress"

The content field is empty because the fix is adding a relation (backlink), not body content. /bedrock:preserve handles adding the wikilink in B's body or frontmatter.

Capability 2 fixes (concept creation)

For each confirmed concept candidate:

- type: concept
  name: "<concept-slug>"
  action: create
  content: "<brief definition derived from the recurring mentions>"
  relations:
    <referencing entity types>: ["<entity-1>", "<entity-2>", ...]
  source: "compress"

Plus, for each referencing entity that should link to the new concept:

- type: <entity's type>
  name: "<entity's name>"
  action: update
  content: ""
  relations:
    concepts: ["<concept-slug>"]
  source: "compress"

Capability 3 fixes (entity misalignment)

For each misaligned entity:

If current type is fleeting (promotion):

- type: <proposed new type>
  name: "<new entity name in correct format>"
  action: create
  content: "<content migrated from the fleeting note>"
  relations:
    <inferred relations>: [...]
  source: "compress"
- type: fleeting
  name: "<original fleeting note name>"
  action: update
  content: ""
  relations: {}
  source: "compress"
  metadata:
    status: "promoted"
    promoted_to: "[[<new entity name>]]"

If current type is NOT fleeting (recategorization):

- type: <proposed new type>
  name: "<new entity name in correct format>"
  action: create
  content: "<content from the misaligned entity>"
  relations:
    <inferred relations>: [...]
  source: "compress"

Add a consolidation callout in the original entity (via update):

- type: <current type>
  name: "<original entity name>"
  action: update
  content: "> [!info] Content recategorized to [[<new entity name>]]\n> This entity was recategorized by /bedrock:compress. See [[<new entity name>]] for the current version."
  relations:
    <new type plural>: ["<new entity name>"]
  source: "compress"

Capability 4 fixes (create missing entities)

For each missing entity:

- type: <inferred type>
  name: "<entity-slug>"
  action: create
  content: "<aggregated context from all mentions>"
  relations:
    <mentioning entity types>: ["<entity-1>", "<entity-2>", ...]
  source: "compress"

Plus, for each mentioning entity (to establish backlinks):

- type: <entity's type>
  name: "<entity's name>"
  action: update
  content: ""
  relations:
    <new entity's type plural>: ["<entity-slug>"]
  source: "compress"

Capability 5 fixes (misnamed entities)

For alias additions:

- type: <entity's type>
  name: "<canonical entity name>"
  action: update
  content: ""
  relations: {}
  source: "compress"
  metadata:
    aliases: ["<existing aliases>", "<new variant name>"]

For each file where the variant was found (to add the wikilink):

- type: <entity's type>
  name: "<entity where variant was found>"
  action: update
  content: ""
  relations:
    <canonical entity's type plural>: ["<canonical entity name>"]
  source: "compress"

For entity merges (two files for the same real-world entity):

- type: <canonical entity's type>
  name: "<canonical entity name>"
  action: update
  content: "<merged content from both entities>"
  relations:
    <merged relations from both>: [...]
  source: "compress"
  metadata:
    aliases: ["<combined aliases from both entities>"]

Add a consolidation callout in the secondary entity:

- type: <secondary entity's type>
  name: "<secondary entity name>"
  action: update
  content: "> [!info] Content consolidated in [[<canonical entity name>]]\n> This entity has been consolidated by /bedrock:compress. See [[<canonical entity name>]] for the merged version."
  relations:
    <canonical entity's type plural>: ["<canonical entity name>"]
  source: "compress"

4.2 Invoke /bedrock:preserve

Use the Skill tool to invoke /bedrock:preserve --vault <VAULT_NAME> passing the compiled structured entity list as argument. The --vault <VAULT_NAME> flag ensures preserve writes to the same vault.

Include source: "compress" for all entities so /bedrock:preserve records provenance.

If running in cron mode (autonomous capabilities):

• Add to the invocation prompt: "Autonomous mode — do not ask for confirmation, process directly."

4.3 Await result

/bedrock:preserve returns:

• List of created/updated entities
• Commit hash (if there was a commit)
• Any errors or warnings

Record the result for use in the final report (Phase 5).

---

Phase 5 — Final Report

Present to the user:

## /bedrock:compress — Report

### Mode: interactive / cron

### Alignment fixes applied
| # | Capability | Findings | Fixed | Queued |
|---|---|---|---|---|
| 1 | Broken backlinks | N | M | — |
| 2 | Concept match | N | M | P (cron) |
| 3 | Entity misalignment | N | M | P (cron) |
| 4 | Duplicated entities | N | M | — |
| 5 | Misnamed entities | N | M | P (cron) |

**Total:** N findings, M fixed, P queued

### Entities processed (via /bedrock:preserve)
| Type | Name | Action |
|---|---|---|
| <type> | <name> | create / update |
| ... | ... | ... |

### Queued proposals (cron mode only)
- Created fleeting note: [[<YYYY-MM-DD>-compress-proposals]]
- Contains N proposals for capabilities 2, 3, 5
- Review and run `/bedrock:compress` in interactive mode to execute

### Git
- Commit: <hash from /bedrock:preserve>
- Push: success / failed (reason)

### Suggestions
- Run `/bedrock:healthcheck` for a full vault health report
- [additional suggestions based on findings]

If no fixes were applied (user refused all, or no findings): Present only the summary table with zero counts.

---

Error Handling

Situation	Action
Empty vault (no entities)	Report "No entities found in the vault." and end
No findings across all 5 capabilities	Report "Vault is aligned." and end
User refuses all findings (interactive)	Report "No changes made." and end
Error reading entity	Skip entity, warn in the report
/bedrock:preserve fails	Report the error, list what was NOT processed
Entity without frontmatter	Skip entity, warn in the report
--mode argument not recognized	Default to interactive, warn the user

---

Critical Rules

Rule	Detail
All writes via /bedrock:preserve	NEVER use Write or Edit on entity files. Invoke /bedrock:preserve via the Skill tool.
Mechanical vs. semantic split	Capabilities 1, 4 = mechanical (autonomous in cron). Capabilities 2, 3, 5 = semantic (queued in cron, confirmed in interactive).
User confirmation in interactive	ALWAYS wait for explicit confirmation before delegating to /bedrock:preserve in interactive mode.
Append-only for people/teams/topics	When fixing entities of these types, NEVER delete existing content. Add callouts and new links only.
Actors allow free merge	Actor bodies can be modified freely. Frontmatter is merge-only (never delete fields).
Never remove wikilinks	When fixing backlinks or renaming, ADD new links. Never remove existing ones.
Entity definitions are authoritative	Capabilities 2 and 3 MUST read entity definitions from the plugin directory. Do not hardcode classification heuristics.
3+ threshold	Capabilities 2 and 4 require a term/name to appear in 3+ different entities before flagging.
Provenance	All entities delegated to /bedrock:preserve use source: "compress".
MCP in main context	Do NOT use subagents for MCP calls — permissions are not inherited.
Sensitive data	NEVER include credentials, tokens, passwords, PANs, CVVs.
Vault resolution first	Resolve VAULT_PATH before any file operation or git command — never assume CWD is the vault
All git commands use git -C <VAULT_PATH>	Never assume CWD is the vault
All entity paths use <VAULT_PATH>/ prefix	<VAULT_PATH>/actors/, not actors/
Pass --vault to /preserve	ALWAYS include --vault <VAULT_NAME> when delegating to /bedrock:preserve