Mantis Researcher (/mantis-researcher)

System Goal

Resilience Code Auditor. Performs rapid triage and deep-dive reviews of source files to identify boundary checks, preconditions, missing sanitization, and interface violations.

Command Definition

Command:
```
/mantis-researcher
```
Description: Audits production source code files based on the strategy in
```
workspace/plan.json
```
.
Arguments (optional; supplied by the orchestrator, consumed by Block A):
- ```
--snapshot_root
```
  /
```
SNAPSHOT_ROOT
```
  : absolute path to the pinned, read-only code snapshot for this pass. This is the CODE_ROOT that all snapshot-relative path fields resolve against (Block A step 1b).
- ```
--snapshot_id
```
  /
```
SNAPSHOT_ID
```
  : the pass snapshot identifier. Used for the sentinel check (Block A step 2) and stamped verbatim into every finding's
```
discovery_commit
```
  .
- ```
--state_root
```
  : absolute path to the
```
workspace/
```
  state directory (
```
plan.json
```
  ,
```
.mantis_state.json
```
  ,
```
findings/
```
  ,
```
kb/
```
  ). State paths are STATE-RELATIVE and are NEVER prefixed with CODE_ROOT (Block A step 3).
- ```
--target_root
```
  (authoritative override, Block A step 1a) is also honored if supplied.
- All flags absent -> DEGRADED/legacy mode: CODE_ROOT falls back to the current directory,
```
snapshot_pinned
```
  is treated as false, and behavior matches today's exactly (no
```
discovery_commit
```
  is written).

Input/Output Contract

Reads:
- ```
workspace/plan.json
```
  (falls back to codebase sweep if missing/empty).
- ```
workspace/.mantis_state.json
```
  (to track current loop pass).
- referenced Markdown files in
```
"kb_references"
```
  (e.g.
```
workspace/kb/entities/*.md
```
  ).
- Target source code files.
- ```
workspace/kb/structural_index/manifest.json
```
  (to check structural index availability/status).
- ```
workspace/helpers/query_structural_index.py
```
  (to invoke bounded structural-index queries).

Writes:

Raw finding files to

workspace/findings/<uuid>.json

(creates

workspace/findings/

if missing).

Preconditions:
- Target files must be accessible.
Idempotency Guarantee:
- Writes new findings as separate files with unique UUIDs. Rely on
```
mantis-dedupe
```
  to cluster and merge duplicate findings on subsequent steps.

Instructions

Step 0: Locator Resolution (Snapshot-Aware Path Handling)

Run this BEFORE the numbered research steps below. It fixes the single CODE_ROOT that every

target_files

code_paths

reference in this stage resolves against, so all sub-agents audit the same pinned snapshot.

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.

Skill-specific notes for the researcher:

The researcher is a CODE-READING stage, so Block A step 0's findings-only skip does NOT apply here — you MUST resolve CODE_ROOT and honor the sentinel.
```
workspace/plan.json
```
```
target_files
```
and finding
```
code_paths
```
are SNAPSHOT-RELATIVE: resolve them under CODE_ROOT (Block A step 3).
```
kb_references
```
,
```
workspace/plan.json
```
,
```
workspace/.mantis_state.json
```
, and everything under
```
workspace/findings/
```
are STATE-RELATIVE: read/write them under --state_root, NEVER under CODE_ROOT.
Never write, compile, or generate anything under CODE_ROOT when pinned (Block A step 4).

Perform a thorough memory-safety, logical-correctness, and robustness review of the targeted codebase.

Execute the research stage as follows:

Load Reviewing Plan & Context: Read the active pass number from
```
workspace/.mantis_state.json
```
and resolve the current ISO 8601 timestamp. Read the
```
workspace/plan.json
```
file to retrieve the target investigations. If
```
workspace/plan.json
```
is missing or empty, perform a general list of the directories and review any primary source files. If the investigation contains a
```
"kb_references"
```
array, explicitly read those Markdown files (e.g.,
```
workspace/kb/entities/auth.md
```
) to gain compounded historical context before you begin auditing the
```
"target_files"
```
. Also read
```
active_snapshot
```
from
```
workspace/.mantis_state.json
```
(
```
root
```
,
```
snapshot_id
```
,
```
snapshot_pinned
```
). Hold
```
active_snapshot.snapshot_id
```
in memory: it is the value you will stamp into every finding's
```
discovery_commit
```
(see Findings Schema Format). If
```
active_snapshot
```
is absent or
```
snapshot_pinned
```
is false, you are in DEGRADED/legacy mode — do NOT stop (Block A step 1d); you will simply omit
```
discovery_commit
```
.
Sub-Agent Delegation (Wave-Based Swarm Parallelization): If the CLI or agent platform supports spawning sub-agents (e.g., using specialized sub-agent tools or multi-agent orchestrator directives):
- Do not execute investigations sequentially if sub-agents are supported. Split the investigations in
  workspace/plan.json
  into parallel waves to maximize throughput and context efficiency.
- Wave 1: Lightweight Rapid Triage (Concurrency Peak): Spawn concurrent, lightweight sub-agents (e.g. up to 10-20 in parallel) to sweep all files listed in
  workspace/plan.json
  . Each sub-agent should only output a fast classification:
  {"potentially_flawed": true/false, "reason": "..."}
  .
- Wave 2: Deep Security Flaw Hotspot Audits & Parallel Trajectory Search: Collect all files flagged in Wave 1. Spawn a wave of concurrent deep auditor sub-agents (e.g. up to 4-8 in parallel) to focus exclusively on those identified hotspots. For particularly complex files, spawn multiple subagents targeting the same file using either different prompt constraints or a diverse set of less expensive LLMs to explore parallel attack vectors. Rely on the subsequent deduplication stage to merge any overlapping findings.
- Token Optimization (Distributed Writes): Instruct the Wave 2 sub-agents to generate unique UUIDs and write their findings directly to individual
  workspace/findings/<id>.json
  files on disk. Do not ask them to return the full JSON payload in their messages back to you, as aggregating them will blow out your context window. Ask them to only return the list of UUIDs they created.
- Snapshot Isolation (Wave Pinning) — MANDATORY: Pass the SAME
  --snapshot_root
  (CODE_ROOT resolved in Step 0) and the same
  --snapshot_id
  value to EVERY Wave-1 and Wave-2 sub-agent, and instruct each of them to obey Block A (resolve
  target_files
  /
  code_paths
  under that CODE_ROOT, honor the sentinel). Any Wave-2 sub-agent that writes a finding MUST stamp
  discovery_commit
  with that snapshot_id, exactly as specified in the Findings Schema Format. Sub-agents MUST NOT run
  git pull
  /
  fetch
  /
  checkout
  /
  reset
  ,
  hg pull
  /
  update
  ,
  repo sync
  , or any command that changes the working tree or switches revisions — the snapshot is immutable for the whole pass. A sub-agent that cannot see the snapshot must report that, not re-sync.
- If sub-agents or concurrency are not supported by the current environment, fall back to performing the sweeps and deep-dives sequentially.
- Structural Index (HINT-only enhancement): When a structural index is available (
  workspace/kb/structural_index/manifest.json
  exists), use it to SUPPLEMENT the wave-based swarm above. The structural index decides ORDER, never MEMBERSHIP. It MUST NEVER replace the exhaustive Step-3 call-site sweep.
  - Resolution-first protocol (MANDATORY before any structural query):
    1. Resolve the symbol first:
      python3 workspace/helpers/query_structural_index.py resolve_symbol --name "<function_name>" [--language "<lang>"] [--file "<path>"] --state_root <state_root>
    2. If the response has
      ambiguous: true
      , investigate ALL matched symbols — never silently pick one. Narrow with
      --file
      /
      --language
      if possible, or schedule investigations for every matched symbol.
    3. Use the resolved
      symbol_id
      for bounded queries:
      python3 workspace/helpers/query_structural_index.py find_callers --symbol_id "<id>" --limit 100 --offset 0 --state_root <state_root>
  - Coverage-aware interpretation: Check
    coverage.partition_status
    in every structural index response:
    - complete
      +
      precision == semantic
      + empty results = "no indexed callers" (authoritative for indexed code — still run grep per the HINT-only rule).
    - complete
      +
      precision != semantic
      + empty results = "no indexed callers" — NOT authoritative. MUST run exhaustive grep.
    - partial
      /
      empty
      /
      failed
      + empty results = "not fully indexed" — MUST run exhaustive grep.
    - Use the
      precision
      and
      backend
      fields on every result to weight trust (
      semantic
      >
      typecheck
      >
      ast
      >
      symbol-only
      >
      heuristic
      >
      deferred
      >
      coverage-only
      ).
  - Wave 1 (Rapid Triage): Use
    find_callers()
    to SUPPLEMENT grep as a ranking HINT — ORDER, never MEMBERSHIP. Structural index results prioritize which files to flag as
    potentially_flawed
    ; they MUST NEVER replace the exhaustive Step-3 call-site sweep. Audit the union of grep results and structural index results.
  - Wave 2 (Deep Audit): Use
    get_function_boundary(file, line)
    to start with the enclosing function, then expand to callers/callees/file as needed for deep dive context.
  - Graceful degradation: If the structural index is absent (no
    manifest.json
    ), empty, or the query helper is missing, fall back to grep-based discovery (today's behavior). The structural index is a coverage HINT only.
Exhaustive Interface and Call-Site Reviewing: If a target source file defines public or API functions (such as numeric parsers, decoders, encoders, or converters) that document explicit size constraints or safety requirements (e.g., expecting callers to allocate buffers of a certain size):
- Run a repo-wide grep for the function name to build the exhaustive set of candidate call-sites — this is the mandatory floor. Then use the structural index query helper (
```
resolve_symbol
```
  then
```
find_callers
```
  ) to RANK and prioritize which call-sites to audit first (the index distinguishes actual calls from comments/strings/variable names). Audit the union of both result sets — the structural index may miss macro-based calls, function pointers, and dynamic dispatch, so grep remains the floor.
- Search the codebase to find and review all call-sites of these functions across the entire repository to ensure the safety contracts are respected globally.
- Read the calling files and verify if every call-site strictly adheres to input constraints, properly manages bounds, and checks sizes.
- Flag any discrepancies as contract alignment bugs or missing checks.
Unconstrained / Exploratory Investigations: If the investigation plan in
```
workspace/plan.json
```
contains instructions or a question explicitly asking for an unconstrained sweep, adversarial audit, or random exploration:
- Ignore existing assumptions of safety and documented trust boundaries in
```
workspace/kb/THREAT_MODEL.md
```
  .
- Treat all inputs and boundaries as untrusted and potentially malformed.
- Analyze implementation from scratch with full freedom and autonomy.
- If it is a random exploration/digging task with minimal instructions, focus on mapping the behavior of the target files, identifying key entry points, and looking for unexpected side effects or boundary cases without being constrained by a specific threat model.
Compile and Write Findings: Instead of a single monolithic file, create a
```
workspace/findings/
```
directory if it does not exist. For each potential finding, generate a unique UUID and write a valid JSON object into an individual file named
```
workspace/findings/<id>.json
```
. This keeps findings isolated and prevents token limit issues during subsequent analysis. Do not include any text before or after the JSON in the files.
Signature & Lineage Computation (Step 5a):
For each finding, compute
```
signature
```
,
```
lineage_id
```
, and optionally
```
cwe
```
BEFORE writing the JSON file:
1. cwe
  (optional): If the vulnerability maps to a known CWE, set the
  cwe
  field to the identifier (e.g.,
  "CWE-787"
  ,
  "CWE-416"
  ). If no CWE applies, omit the field. This is an input to the signature.
2. Compute
  signature
  (deterministic content-identity hash):
  - normalized_title
    = finding
    title
    , lowercased, with ALL non-alphanumeric characters stripped (ASCII
    [a-zA-Z0-9]
    only; all other characters including Unicode letters, punctuation, and spaces are removed). If stripping leaves
    normalized_title
    EMPTY (e.g. a title composed entirely of non-ASCII/Unicode characters), set
    normalized_title
    = the first 16 hex chars of
    sha256(<original raw title as UTF-8 bytes>)
    so two distinct non-ASCII titles do not collide on the empty string.
  - cwe_part
    = the finding's
    cwe
    field if present and non-null, else the empty string.
  - primary_target
    = first
    code_paths
    entry with trailing
    :line
    stripped (e.g.,
    src/auth.c:145
    →
    src/auth.c
    ). If
    code_paths
    is empty, or the first entry is a non-source LOCATOR (URL containing
    ://
    , or a non-file symbol/offset per Block A step 3), use the empty string. Order
    code_paths
    deterministically (primary sink first, kept stable across passes) so
    primary_target
    — and thus the
    signature
    — does not drift between passes. (If the order is unstable the only cost is a missed lineage inheritance → the finding is over-reported as new, never hidden — but stable order preserves the cross-pass fold.)
  - If
    primary_target
    is non-empty:
    signature
    = first 16 hex characters of
    sha256(normalized_title + "|" + cwe_part + "|" + primary_target)
    .
  - If
    primary_target
    is empty:
    signature
    = first 16 hex characters of
    sha256(normalized_title + "|" + cwe_part + "|" + sorted(code_paths).join(","))
    .
  - Compute the signature ONCE at finding creation and NEVER recompute, edit, or invent it (same rule as
    discovery_commit
    ).
3. Compute
  lineage_id
  (cross-pass lineage chain):
  - Scan
    workspace/archive/findings_pass_*/
    and
    workspace/archive/loop*_findings/
    for any archived finding JSON whose
    signature
    field equals this finding's computed
    signature
    .
  - If a match is found:
    lineage_id
    = the archived ancestor's
    lineage_id
    (inherit the lineage chain so consumers can fold across passes). If MULTIPLE archived findings share the same signature, inherit from the MOST RECENT (highest pass number) ancestor. All ancestors with the same signature SHOULD share the same lineage_id; if they don't, inherit from the most recent one and log a warning.
  - If no match by exact signature: attempt a basename rename fallback for TRUE renames ONLY. Do NOT recompute the signature (it is computed ONCE at creation and never recomputed — invariant #4). Instead:
    1. Compute the CURRENT finding's basename: take
      primary_target
      (the first
      code_paths
      entry with trailing
      :line
      stripped, already computed for the signature at step 2) and take its basename (e.g.
      src/auth.c
      →
      auth.c
      ). If
      primary_target
      is empty (non-source LOCATOR or empty code_paths), SKIP this fallback — go to fresh UUIDv4 below.
    2. For each archived finding located in step 3's archive scan: reconstruct the ARCHIVED finding's basename from its stored
      code_paths[0]
      (strip the trailing
      :line
      , take the basename — e.g.
      lib/old_auth.c:88
      →
      old_auth.c
      ). Do NOT recompute the archived finding's signature and do NOT compare signatures; compare the two basenames as STRINGS.
    3. Inherit an ancestor's
      lineage_id
      via this fallback ONLY IF (i) the basenames match AND (ii) the ancestor's full
      primary_target
      (its
      code_paths[0]
      with
      :line
      stripped) NO LONGER EXISTS on the current snapshot (check that the old full path is absent under CODE_ROOT — this distinguishes a real rename from a second, independent file that merely shares a basename). If MULTIPLE archived ancestors satisfy (i) and (ii), inherit from the MOST RECENT (highest pass number). When you inherit via basename, ALSO add a finding history note
      lineage-via-basename-rename
      so downstream consumers treat the link as basename-derived (the report folds two findings only when their full
      signature
      s ALSO match per the SAME-BUG predicate, so a basename-derived lineage link never collapses distinct bugs).
    4. If the old full path still exists on the current snapshot, do NOT inherit — treat as no match (fresh UUIDv4 below).
  - If no match by either exact signature or basename rename:
    lineage_id
    = a fresh UUIDv4.
  - These are STATE-RELATIVE paths (Block A step 3) — read under
    --state_root/workspace/archive/
    , NEVER under CODE_ROOT.
4. Write all three fields (
  cwe
  ,
  signature
  ,
  lineage_id
  ) into the finding JSON alongside
  discovery_commit
  .
Mode-independence: Unlike
```
discovery_commit
```
(which is omitted in DEGRADED/legacy mode),
```
signature
```
and
```
lineage_id
```
are ALWAYS computed — they are content-identity fields, not snapshot-identity. They work regardless of whether the snapshot is pinned, unpinned, or absent (MODE-OFF). This is a deliberate Phase-3 improvement: in MODE-OFF, the finding JSON now carries 2–3 extra optional keys (
```
cwe
```
,
```
signature
```
,
```
lineage_id
```
) that did not exist in Phase 1. This does NOT change the snapshot model (no
```
active_snapshot
```
, no sync, no pin — the 3-state rule is unaffected). The dedupe MODE-OFF fallback now prefers
```
signature
```
over
```
stable_key
```
when present, which is strictly MORE discriminating (signature adds
```
cwe
```
to the title+path mix), so it can only SPLIT entries that
```
stable_key
```
would have merged (fresh budgets, more conservative = safe) — it can never produce a false merge or suppress a legitimate finding. Absent
```
signature
```
→ today's
```
stable_key
```
behavior exactly.
Missing or unreadable target file: If a path in
```
target_files
```
does not exist or cannot be read under CODE_ROOT (e.g. it was deleted or renamed since the plan was written), do NOT fabricate a finding, a line number, or file contents. Skip that target and record the skip plainly in the
```
description
```
of any finding it relates to (or omit it entirely). Never invent code you did not read.
Non-source targets: For a non-source LOCATOR (binary, firmware, or a URL endpoint — see Block A step 3), the
```
code_paths
```
entry MUST be a STABLE LOCATOR (symbol name, offset, or the bare path) WITHOUT a
```
:line
```
suffix. Do not attach a fabricated line number to a target you cannot open as text.

Findings Schema Format (Per File)

json

{
  "id": "A unique identifier generated for this finding (e.g., a UUID or random hash). This must be included and match the filename.",
  "title": "Authorization bypass or Memory bounds violation in [function_name]",
  "description": "Thorough root cause analysis detailing why the function is flawed under untrusted input.",
  "impact": "Exploit outcome (e.g., Privilege escalation, Memory corruption, Data exfiltration).",
  "severity": "CRITICAL / HIGH / MEDIUM / LOW",
  "privileges_required": "NONE / LOW / HIGH",
  "attacker_position": "EXTERNAL / INTERNAL_NETWORK / IN_CLUSTER / LOCAL / HOST_SYSTEM / SUPPLY_CHAIN / PHYSICAL_TEMPORARY / PHYSICAL_LONG_TERM",
  "user_interaction": "NONE / REQUIRED",
  "status": "PROVISIONALLY_VALID",
  "code_paths": ["SNAPSHOT-RELATIVE path under CODE_ROOT, e.g. 'relative/file/path.c:145'. For a NON-SOURCE target (binary/firmware/URL, per Block A step 3) use a STABLE LOCATOR (symbol name, offset, or bare path) WITHOUT a fabricated ':line'. Never invent a line number."],
  "discovery_commit": "The active_snapshot.snapshot_id read from workspace/.mantis_state.json at the start of this pass (Step 1). REQUIRED and NON-EMPTY whenever the snapshot is pinned: copy it VERBATIM, set it exactly ONCE at finding creation, and never recompute, edit, or invent it. OMIT this key entirely (do not write \"\" or null) if active_snapshot is absent or snapshot_pinned is false (DEGRADED/legacy mode).",
  "cwe": "CWE-787 (optional; omit if no CWE applies)",
  "signature": "First 16 hex chars of sha256(normalized_title + '|' + cwe_part + '|' + primary_target). Computed once at creation, never recomputed.",
  "lineage_id": "UUIDv4, or inherited from an archived finding with the same signature. Computed once at creation.",
  "mitigation": "Recommended corrective modification.",
  "history": [
    {
      "stage": "researcher",
      "action": "created",
      "details": "Initial audit finding recorded.",
      "pass_number": <current_pass_number>,
      "timestamp": "<current_iso8601_timestamp>"
    }
  ]
}

discovery_commit
rule (set once, at creation): This stage is the creation site for

discovery_commit

. When the snapshot is pinned, every finding you (or your Wave-2 sub-agents) write MUST carry a non-empty

discovery_commit

equal to

active_snapshot.snapshot_id

. Downstream stages treat an absent

discovery_commit

as NOT_MATCHED (the conservative branch), so writing an empty string or a wrong value would silently corrupt matching — never do it. In DEGRADED/legacy mode (no

active_snapshot

, or

snapshot_pinned

false) omit the key so behavior matches today's pipeline.

signature
/
lineage_id
rule (set once, at creation): These fields are ALWAYS computed (unlike

discovery_commit

, which is omitted in degraded mode). The signature is a deterministic hash of the finding's content identity; the lineage_id chains the finding to its archived ancestors. Downstream consumers (dedupe, chain, report, reproduce) key on signature/lineage with UUID fallback: absent

signature

→ today's UUID behavior exactly (no silent wrong result).

Ensure all individual finding files are written to the

workspace/findings/

directory. When complete, notify the user.

mantis-researcher

NPX Install

Tags

SKILL.md Content