Wiki Dedup

Wiki Dedup — Identity Resolution and Page-Level Deduplication

You are finding and merging wiki pages that cover the same concept under different names. This is a write-heavy, potentially destructive skill — page merges cannot be automatically undone. Work carefully and confirm before acting in merge mode.

Follow the Retrieval Primitives table in llm-wiki/SKILL.md. The candidate-detection pass uses only frontmatter and titles (cheap). Only open full page bodies for confirmed candidate pairs.

Before You Start

Writing profile: Before drafting or rewriting natural-language Markdown, read and apply the Writing Profile Resolution section in llm-wiki/SKILL.md. Framework schema, provenance, safety, and operation-specific requirements take precedence. WRITING.md preferences apply only to newly drafted or rewritten natural-language Markdown; preserve source content and structured records.

1. Resolve config — follow the Config Resolution Protocol in llm-wiki/SKILL.md (inline @name override → walk up CWD for .env → global config → prompt setup). This gives OBSIDIAN_VAULT_PATH and OBSIDIAN_LINK_FORMAT.
2. Read index.md to get the full page inventory with one-line descriptions and tags.
3. Read log.md briefly — if a dedup run just happened, note what was already merged.

Modes

If the user doesn't specify, run in Audit mode and present findings before asking whether to proceed.

Step 1: Build the Page Registry

Glob all .md files in the vault (excluding _archives/, _raw/, .obsidian/, index.md, log.md, hot.md, _insights.md, and any file that contains redirects_to: in its frontmatter — those are already merged redirect stubs).

For each remaining page, extract from frontmatter:

• node_id — relative path from vault root, without .md
• title — frontmatter title field
• aliases — frontmatter aliases list (may be absent)
• tags — frontmatter tags list
• category — directory prefix

Build a lookup table: node_id → {title, aliases, tags, category, summary}.

Step 2: Detect Candidate Pairs

For every pair of pages in the registry, compute a similarity score using these signals:

2a. Title similarity signals

Composite title score = min(max(token_overlap, edit_distance, substring), 0.65) + alias_cross_bonus.

You don't need exact arithmetic — make a confident judgement about degree of similarity.

Title extraction note: Some pages use YAML block scalars (title: >- or title: |). When the title: value is >-, >, |, or |-, the actual title is on the next indented line — read it from there. Never compare the literal string >- as a title.

2b. Semantic signals (cheap pass)

2c. Threshold

Flag pairs with composite score ≥ 0.75 as candidates. Pairs scoring 0.90+ are high-confidence.

Score ranges → confidence labels:

Only carry HIGH and MEDIUM candidates into Step 3.

2d. Quick exit rule

If the vault has fewer than 10 pages, skip the pair loop and report "vault too small to have meaningful duplicates". If the vault has more than 500 pages, process candidates in batches of 50 pairs — pause and report progress between batches.

Step 3: Semantic Verdict

For each candidate pair (sorted by score descending):

1. Read both pages in full (full page read — justified because candidate pool is small).
2. Ask: are these pages covering the same concept, or are they distinct?

Assign one of three verdicts:

Attach a short reason to each verdict (one sentence). This appears in the report and the log.

Step 4: Audit Report

Always produce this report, even in merge/auto-merge mode (so the user sees what will happen):

## Wiki Dedup Report

### High-Confidence Candidates (score ≥ 0.90): N pairs

| Score | Page A | Page B | Verdict | Reason |
|---|---|---|---|---|
| 0.95 | `concepts/rsc.md` | `concepts/react-server-components.md` | merge | "RSC" is the abbreviation; both pages cover identical material |
| 0.91 | `entities/vaswani-2017.md` | `references/attention-is-all-you-need.md` | keep-separate | One is a person stub, one is a paper reference |

### Medium-Confidence Candidates (score 0.75–0.89): N pairs

| Score | Page A | Page B | Verdict | Reason |
|---|---|---|---|---|
| 0.82 | `concepts/fine-tuning.md` | `concepts/finetuning.md` | merge | Same concept, hyphenation variant |

### Needs Human Review: N pairs

| Score | Page A | Page B | Reason |
|---|---|---|---|
| 0.78 | `concepts/agents.md` | `concepts/autonomous-agents.md` | Substantial overlap but "agents" may intentionally be broader |

### Summary
- Pages scanned: N
- Candidate pairs found: M
- Recommended merges: X
- Keep separate: Y
- Needs review: Z

In Audit mode, stop here and ask: "Run --merge to interactively merge the recommended pairs, or --auto to merge all high-confidence ones automatically?"

Step 5: Merge

Pre-write snapshot — before the first file write, check whether the vault itself is the root of a Git repository. Merely being a subdirectory of a larger repository does not qualify: running git add -A there could capture unrelated files. If the vault is not a standalone Git repository, skip this step silently — no nagging, no suggesting git init.

VAULT_REAL_PATH=$(cd "$OBSIDIAN_VAULT_PATH" && pwd -P)
VAULT_GIT_ROOT=$(git -C "$OBSIDIAN_VAULT_PATH" rev-parse --show-toplevel 2>/dev/null || true)
SNAPSHOT_SHA=""

if [ -n "$VAULT_GIT_ROOT" ] && [ "$VAULT_GIT_ROOT" = "$VAULT_REAL_PATH" ]; then
  if git -C "$OBSIDIAN_VAULT_PATH" diff --quiet \
    && git -C "$OBSIDIAN_VAULT_PATH" diff --cached --quiet \
    && [ -z "$(git -C "$OBSIDIAN_VAULT_PATH" ls-files --others --exclude-standard)" ]; then
    SNAPSHOT_SHA=$(git -C "$OBSIDIAN_VAULT_PATH" rev-parse HEAD)
  else
    if ! git -C "$OBSIDIAN_VAULT_PATH" add -A; then
      echo "Pre-write snapshot failed; abort the skill without writing any vault files." >&2
      exit 1
    fi
    if ! git -C "$OBSIDIAN_VAULT_PATH" commit -m "pre-wiki-dedup snapshot" --quiet; then
      echo "Pre-write snapshot failed; abort the skill without writing any vault files." >&2
      exit 1
    fi
    SNAPSHOT_SHA=$(git -C "$OBSIDIAN_VAULT_PATH" rev-parse HEAD)
  fi
fi

The clean-repository branch deliberately avoids calling git commit, so "nothing to commit" is not treated as an error. If git add or git commit fails, stop before editing the vault; never continue without the promised snapshot.

If SNAPSHOT_SHA is non-empty and the skill writes files, include the SHA in the final report. To discard the entire run, after confirming there are no later changes worth keeping, the user can run:

git -C "$OBSIDIAN_VAULT_PATH" reset --hard "$SNAPSHOT_SHA"
git -C "$OBSIDIAN_VAULT_PATH" clean -fd

For each merge verdict pair (in merge or auto-merge mode):

In merge mode: show the pair and verdict, then ask: "Merge [Page A] into [Page B]? (yes/skip/review)". Skip on anything other than yes.

In auto-merge mode: only process HIGH-confidence (score ≥ 0.90) merges without prompting.

5a: Pick the canonical page

Apply these tiebreakers in order until one wins:

1. More incoming wikilinks — grep the vault for [[node_id]] references; higher count wins
2. Richer content — longer page body (more lines) wins
3. More sources — larger sources: list wins
4. Title length — longer, more descriptive title wins (e.g. "React Server Components" beats "RSC")
5. Alphabetical — earlier title wins

The canonical page is the survivor. The other page becomes the secondary (to be merged in, then replaced with a redirect stub).