Deduplicator (/mantis-dedupe)

System Goal

Duplicate Finding Merger. Evaluates lists of raw findings to cluster and consolidate identical or highly overlapping issues into singular, descriptive records.

Command Definition

Command:
```
/mantis-dedupe
```
Description: Consolidates raw security findings to eliminate redundant reports.
Arguments (optional; supplied by the orchestrator, consumed by Block A):
```
--snapshot_root
```
/
```
--snapshot_id
```
/
```
--state_root
```
. All absent -> MODE-OFF/legacy mode (behaves as today; snapshot gating disabled).

Input/Output Contract

Reads:
- ```
workspace/findings/
```
  (raw finding JSON files, ignoring
```
.trash/
```
  ).
- ```
workspace/archive/findings_pass_*/*.json
```
  and
```
workspace/archive/loop*_findings/*.json
```
  (to skip findings already evaluated and triaged in previous passes).
- ```
workspace/.mantis_state.json
```
  (to track current loop pass).
Writes:
- Moves duplicate findings to
```
workspace/findings/.trash/
```
  after setting
```
"status": "DUPLICATE"
```
  and
```
"duplicate_of"
```
  .
- Sets
```
"possible_duplicate_of"
```
  (soft, non-terminal) on NOT_MATCHED matches and stamps
```
"discovery_commit"
```
  on current findings that lack it. Reads
```
active_snapshot
```
  /
```
snapshot_pinned
```
  from
```
.mantis_state.json
```
  .
- Appends transaction logs to
```
workspace/.tx_log.jsonl
```
  .
- Generates/executes merging script
```
workspace/helpers/merge_findings.py
```
  .
- Updates primary finding
```
workspace/findings/<primary_id>.json
```
  (merges fields and history).
Preconditions:
- ```
workspace/findings/
```
  must exist and contain finding files.
Idempotency Guarantee:
- Cross-references against archived findings in
```
workspace/archive/
```
  to filter out any findings already processed in previous passes of this run. Snapshot-gated: a resolved archived finding on a differing snapshot is flagged as POSSIBLE REGRESSION (never silently filtered). Logs transactions to
```
workspace/.tx_log.jsonl
```
  to support tracking and potential rollbacks. Deterministic merging rules implemented in
```
merge_findings.py
```
  .

Instructions

Step 0: Locator Resolution (run first)

LOCATOR RESOLUTION (before reading ANY target code or artifact):
0. ROLE: If this skill NEVER reads target source (report, calibrate, reflect),
   you are a FINDINGS-ONLY stage: skip steps 2-6; still read active_snapshot from
   state for provenance/annotation; NEVER stop merely because a code root is unset.
1. Determine CODE_ROOT, in this priority order:
   a. If --target_root is passed on THIS invocation, CODE_ROOT = --target_root.
      It is AUTHORITATIVE and OVERRIDES SNAPSHOT_ROOT and the state fallback
      (used when a caller hands you a prepared tree, e.g. a patched shadow).
   b. Else if --snapshot_root (or SNAPSHOT_ROOT) is passed, use it.
   c. Else read state_root/workspace/.mantis_state.json (state_root from
      --state_root if passed, else ./workspace/... relative to the current dir)
      -> active_snapshot.root / .snapshot_id / .snapshot_pinned.
   d. Else (no arg AND no readable active_snapshot): CODE_ROOT = current directory,
      treat snapshot_pinned = false (MODE-OFF). Do NOT stop.
2. SENTINEL CHECK (only if snapshot_pinned is true AND you did NOT take path 1a):
   verify CODE_ROOT/.mantis_snapshot_id exists and equals SNAPSHOT_ID. If missing
   or different -> STOP "snapshot sentinel mismatch". (A --target_root tree (1a) is
   deliberately mutated and is sentinel-EXEMPT.)
3. PATH FIELDS:
   - SNAPSHOT-RELATIVE (read under CODE_ROOT): code_paths entries; plan target_files
     that are file paths. Strip ONLY a trailing ":<digits>". A code_paths entry
     containing "://" is a URL/endpoint, NOT a file read. A code_paths entry that is
     NOT of the form <existing-path>:<integer> is a non-source LOCATOR
     (symbol/offset/endpoint): only check that the artifact/symbol exists; skip ALL
     line-range and line-existence logic.
   - STATE-RELATIVE (read/write under state_root/workspace, NEVER prefix CODE_ROOT):
     kb_references, repro_file_path, reattack_file_path, helper scripts, report
     files, and all state/findings JSON.
4. Never WRITE under CODE_ROOT when snapshot_pinned is true. Any command that
   compiles, generates, or writes artifacts MUST run in a PRIVATE SHADOW copy
   (mktemp -d from CODE_ROOT), never with cwd=CODE_ROOT. Read-only inspection may
   cd into CODE_ROOT.
5. VCS-METADATA CARVE-OUT: history-log extraction and any VCS diff/blame command
   run in the LIVE repository root (which still has .git/.hg/.repo), NOT CODE_ROOT
   (the snapshot copy strips VCS metadata). Do NOT stop merely because CODE_ROOT
   lacks .git/.hg/.repo.
6. Every shell command uses ABSOLUTE paths and sets its own working directory on
   that call. Do NOT assume the working directory persists between calls.

[!NOTE] CURRENT-PASS CHECK (defensive; the binding guarantee is on the harness per
mantis-pipeline-adapter
Scenario 2): if
active_snapshot
is present AND
active_snapshot.pass != state.pass_number
, treat the snapshot as STALE for this pass — STOP "stale active_snapshot: pass mismatch" or degrade as HALT (
snapshot_pinned
effectively false: no authoritative verdicts, Block B NOT_MATCHED, reproduce
not_attempted
). This catches a custom harness that preserved
active_snapshot
across the Stage 15 pass increment without re-pinning. The reference meta-agent re-pins every pass, so this check never fires there. Block B itself cannot detect this (it is
snapshot_id
-only, not
pass
-aware).

Notes:

workspace/findings/

workspace/archive/

workspace/.tx_log.jsonl

workspace/helpers/

and

.mantis_state.json

are STATE-RELATIVE (under --state_root). Any code snippet you inspect for a finding is SNAPSHOT-RELATIVE (under CODE_ROOT). Never write under CODE_ROOT.

Review a list of security findings and merge duplicate findings that refer to the exact same security flaw or adjacent code paths.

Execute your task as follows:

Load Raw Findings & Archived Findings Queue:
- List the contents of the directory and read the files in
```
workspace/findings/
```
  . If the directory is empty or does not exist, notify the user and exit.
- Important: Ignore hidden files and directories (such as the
```
.trash/
```
  subdirectory) when listing or processing findings.
- Locate and load all archived finding JSON files from previous loop passes, if they exist, under
```
workspace/archive/findings_pass_*/*.json
```
  and
```
workspace/archive/loop*_findings/*.json
```
  . These files represent vulnerabilities that have already been fully evaluated, triaged, and potentially patched in previous passes.
- Important: Do NOT read or deduplicate against
```
workspace/historical_learnings.jsonl
```
  (VCS history), as we want to catch regressions if old bugs were reintroduced.
Filter Loop Duplicates (snapshot-gated). First, stamp
```
discovery_commit
```
on any CURRENT finding that lacks it, using
```
active_snapshot.snapshot_id
```
from
```
.mantis_state.json
```
(skip when unpinned). Then, for each current finding that matches an archived finding (by
```
code_paths
```
+
```
title
```
similarity), run:
Signature-based candidate matching (Phase 3) — TIGHTENS, never replaces:
```
signature
```
may only PROMOTE a pair to "candidate for the pairwise snapshot check"; it may NEVER by itself cause a hard DUPLICATE/trash. A pair is a candidate for the Pairwise Snapshot Match Check below ONLY if it satisfies BOTH:
- it matches under today's
```
code_paths
```
  +
```
title
```
  similarity, comparing
```
code_paths
```
  entries line-inclusively (WITH their trailing
```
:line
```
  ); AND
- (when both findings have a
```
signature
```
  ) their
```
signature
```
  fields are equal. A
```
signature
```
  match WITHOUT the
```
code_paths
```
  +
```
title
```
  agreement is NOT a duplicate — at most a soft
```
possible_duplicate_of
```
  (keep the finding ACTIVE), never a trash. Rationale:
```
signature
```
  strips the line number and all-but-first
```
code_paths
```
  entry, so two DISTINCT bugs in the same file (e.g.
```
parser.c:100
```
  vs
```
parser.c:900
```
  ) with the same title+CWE share one
```
signature
```
  ; trashing on signature alone would silently delete a real finding. If EITHER lacks
```
signature
```
  , use today's
```
code_paths
```
  +
```
title
```
  similarity matching unchanged.
PAIRWISE SNAPSHOT MATCH CHECK (decides MATCHED vs NOT_MATCHED) — compares the CURRENT finding's
```
discovery_commit
```
against the ARCHIVED finding's
```
discovery_commit
```
for this pair (NOT against
```
SNAPSHOT_ID
```
):
1. If
```
snapshot_pinned
```
  is false AND there is NO
```
active_snapshot
```
  in state (MODE-OFF) -> NOT_MATCHED. Stop. (In HALT —
```
active_snapshot
```
  present but
```
snapshot_pinned=false
```
  — do NOT short-circuit here; fall through to the pairwise comparison below, which will be NOT_MATCHED because the current finding's
```
discovery_commit
```
  is a
```
live:
```
  id that will not equal the archived one.)
2. Read the CURRENT finding's
```
discovery_commit
```
  and the ARCHIVED finding's
```
discovery_commit
```
  :
  - If EITHER is missing, empty, or the literal
    "MIXED"
    -> NOT_MATCHED.
  - If they are NOT byte-for-byte equal to each other -> NOT_MATCHED.
  - If they ARE byte-for-byte equal to each other (both present, non-MIXED) -> MATCHED. There is no other route to MATCHED; never fuzzy-compare. The global "default the field and proceed" backward-compat rule does NOT apply to
    discovery_commit
    : absent = NOT_MATCHED. (There is NO separate "dirty" gate: a dirty tree's SNAPSHOT_ID already embeds the working-tree content hash, so within-pass findings MATCH and cross-pass bare-commit findings do not.) Note: this is a PAIRWISE check (current vs archived), NOT a check against the global
    SNAPSHOT_ID
    — dedupe stamps the current finding's
    discovery_commit
    to
    SNAPSHOT_ID
    in Step 2 above, so a check against
    SNAPSHOT_ID
    would always be MATCHED and would trash reintroduced/regression bugs as DUPLICATE.
Then, using the idempotency rule (Input/Output Contract → Idempotency Guarantee) to avoid double-writes, decide mechanically:
- MATCHED (both present and equal): soft-delete the current finding as a loop-duplicate exactly as before — set
```
"status": "DUPLICATE"
```
  and
```
"duplicate_of": "<archived_uuid>"
```
  , clear
```
possible_duplicate_of
```
  if present, ensure
```
mkdir -p workspace/findings/.trash/
```
  , move it there, and log a
```
loop_filter
```
  transaction in
```
workspace/.tx_log.jsonl
```
  . If the current finding lacks
```
lineage_id
```
  but the archived finding has one, inherit the archived finding's
```
lineage_id
```
  onto the current finding before moving it (so the lineage chain is preserved across the merge).
- NOT_MATCHED (differ, or either absent): do NOT set
```
DUPLICATE
```
  and do NOT move to trash. Keep the current finding ACTIVE and set
```
"possible_duplicate_of": "<archived_uuid>"
```
  (a soft, non-terminal hint). If the current finding lacks
```
lineage_id
```
  but the archived finding has one, inherit the archived finding's
```
lineage_id
```
  onto the current finding (so the lineage chain is preserved for report folding even when the findings are on different snapshots).
[!IMPORTANT] STATUS & DUPLICATE INVARIANTS:
- A finding MUST NOT carry both
  duplicate_of
  and
  possible_duplicate_of
  pointing to the same target UUID.
- status = "DUPLICATE"
  MUST NOT coexist with
  possible_duplicate_of
  pointing to the same target UUID.
- Under NOT_MATCHED (outside the MODE-OFF fallback exception), the finding's
  status
  MUST remain active (e.g.
  VALID
  ,
  PROVISIONALLY_VALID
  ,
  NEEDS_RESEARCH
  ),
  duplicate_of
  MUST NOT be set, and the finding MUST NOT be moved to
  .trash/
  . Setting
  possible_duplicate_of
  is a non-terminal hint only.
- POSSIBLE REGRESSION: if the archived match has a RESOLVED status (
```
patch_status
```
  in {
```
VERIFIED_SECURE
```
  ,
```
MITIGATION_PROPOSED
```
  } OR
```
status
```
  ==
```
FALSE_POSITIVE
```
  OR
```
production_viability
```
  ==
```
NON_VIABLE
```
  ) AND the pair is NOT MATCHED, keep the current finding ACTIVE, add a history note "POSSIBLE REGRESSION vs <archived_uuid>", and do NOT filter it. (A reverted fix re-discovered on new code must never be trashed.)
- EXACT-UUID retry exception (unchanged): if the current finding has the EXACT SAME UUID as the archived one, it was intentionally copied back for a retry — do NOT filter it (keep as-is).
- Permanently-unpinned exception (MODE-OFF only — no
  active_snapshot
  ): if there is NO
```
active_snapshot
```
  in state (MODE-OFF = today's default; a target with no snapshot boundary, e.g. a live endpoint),
```
snapshot_pinned
```
  is false at the PASS level (
```
active_snapshot.snapshot_pinned
```
  — it is NOT a per-finding field) and Block B is uninformative — fall back to today's dedup by
```
signature
```
  if present, else
```
stable_key
```
  = normalized_title + first
```
code_paths
```
  entry including its trailing
  :line
  (line-inclusive, same as Step 2). Rationale: stripping
```
:line
```
  would collapse two DISTINCT bugs in the same file (e.g.
```
parser.c:100
```
  vs
```
parser.c:900
```
  ) with the same title+CWE into one — silently deleting a real finding. Note:
```
signature
```
  itself strips
```
:line
```
  by design (it is a coarse identity for cross-pass lineage, not a dedup key); this fallback therefore prefers
```
signature
```
  only when
```
stable_key
```
  's line-inclusive match ALSO agrees, never on
```
signature
```
  alone. This preserves dedup for targets that can never MATCH. When
```
active_snapshot
```
  IS present but unpinned (HALT mode), this exception does NOT fire: keep the snapshot-gated behavior above (NOT_MATCHED → keep ACTIVE +
```
possible_duplicate_of
```
  , never
```
DUPLICATE
```
  ). POSSIBLE REGRESSION takes precedence over this fallback: a resolved-archived finding paired with a NOT_MATCHED current finding is ALWAYS kept active (never trashed), regardless of mode.
Filter Duplicate Findings in Current Batch: Check the current findings against each other to find duplicates. Two findings are duplicates ONLY if they share the same
```
code_paths
```
entry line-inclusively (WITH trailing
```
:line
```
) AND have the same or highly similar title. If multiple findings refer to the exact same flaw at the same location, they must be merged. Findings at different lines in the same file are DISTINCT — never merge them.
Map/Reduce Chunking Strategy (For Scale): If there are many finding files (e.g., > 20 items), use a Map/Reduce approach to group them by target file or component before checking for overlaps to avoid context window limits.
Token-Optimized Consolidation and Merging: To minimize LLM output tokens and prevent data loss, do not manually rewrite or output the merged JSON files in your response. Instead, follow this pattern:
1. Identify Duplicates: Internally map which findings are duplicates of a primary finding.
2. Reusable Deterministic Scripting (versioned): Write a reusable helper script (e.g.
```
workspace/helpers/merge_findings.py
```
  ) whose FIRST LINE is exactly
```
# MANTIS_HELPER_VERSION = 2
```
  . Before reusing an existing helper, grep its first lines for
```
MANTIS_HELPER_VERSION = 2
```
  ; if that marker is absent or a different integer (a helper left by an older pipeline version), REGENERATE the helper. Only reuse it when the marker matches. The script must follow these deterministic rules:
  - Title: Pick the most comprehensive and descriptive title.
  - ID: Preserve the unique
    "id"
    of the primary finding being kept.
  - Severity: Pick the highest severity level specified among the merged items.
  - Privileges Required: Inherit the most severe privilege requirement (priority:
    NONE
    >
    LOW
    >
    HIGH
    ).
  - Attacker Position: Inherit the most critical position requirement (priority:
    EXTERNAL
    >
    INTERNAL_NETWORK
    >
    IN_CLUSTER
    >
    LOCAL
    >
    HOST_SYSTEM
    >
    SUPPLY_CHAIN
    >
    PHYSICAL_TEMPORARY
    >
    PHYSICAL_LONG_TERM
    ).
  - User Interaction: Inherit the most severe user interaction requirement (priority:
    NONE
    >
    REQUIRED
    ).
  - Code Paths: Collect and deduplicate all file paths and line numbers into a single unique array.
  - Description, Mitigation, & Impact: Concatenate cleanly.
  - History: Concatenate and preserve all
    "history"
    entries from the merged findings. Append a new entry to the
    "history"
    array for this merge action conforming to the schema (containing
    "stage": "dedupe"
    ,
    "action": "merge"
    ,
    "details": "Merged duplicate findings: [comma-separated-ids]"
    ,
    "pass_number": <current_pass_number>
    , and
    "timestamp": "<current_iso8601_timestamp>"
    ).
  - Unknown keys & provenance (MANDATORY): The script MUST copy through EVERY key it does not explicitly handle (including
    discovery_commit
    ,
    repro_snapshot_id
    ,
    patch_base_snapshot
    ,
    possible_duplicate_of
    ,
    signature
    ,
    lineage_id
    ,
    cwe
    ) from the primary finding onto the merged object — never drop unknown fields. It MUST REFUSE to merge two findings whose
    discovery_commit
    values differ (they describe different code versions); leave them separate and log the refusal. When merging findings that all share one
    discovery_commit
    , preserve it unchanged.
3. Execute the Script: Run your script to update the primary finding's file (
```
workspace/findings/<primary_id>.json
```
  ) on disk.
Transactional Staged Clean Up: Do not permanently delete redundant files. Ensure the trash directory exists (e.g.,
```
mkdir -p workspace/findings/.trash/
```
). Before moving, the script must update the duplicate finding files, setting
```
"status": "DUPLICATE"
```
and
```
"duplicate_of": "<primary_uuid>"
```
. Move the merged duplicate
```
.json
```
files to the trash staging directory (
```
workspace/findings/.trash/
```
). For every file moved, append a transaction record to
```
workspace/.tx_log.jsonl
```
.
Transaction Log Schema Format (
```
workspace/.tx_log.jsonl
```
)
Each line must be a self-contained JSON object documenting the transaction:
json
```
{"timestamp": "2026-07-14T15:13:00Z", "action": "loop_filter | dedupe_merge", "primary_uuid": "[UUID] (or null for loop_filter)", "moved_uuid": "[UUID]"}
```
This cleans up the directory for downstream stages while preserving rollback capability.

When complete, notify the user.

mantis-dedupe

NPX Install

Tags

SKILL.md Content

Deduplicator (/mantis-dedupe)

System Goal

Command Definition

Input/Output Contract

Instructions

Step 0: Locator Resolution (run first)

Transaction Log Schema Format (
`workspace/.tx_log.jsonl`
)

mantis-dedupe

NPX Install

Tags

SKILL.md Content

Deduplicator (/mantis-dedupe)

System Goal

Command Definition

Input/Output Contract

Instructions

Step 0: Locator Resolution (run first)

Transaction Log Schema Format (workspace/.tx_log.jsonl)

Transaction Log Schema Format (
`workspace/.tx_log.jsonl`
)