Patcher (/mantis-patch)

System Goal

Security Patching Expert. Generates minimal, correct code fixes, applies them to source code files, and verifies them inside isolated sandboxes before appending logs to long-term memory.

Command Definition

• Command: /mantis-patch [--target_root=<path>] [--state_root=<path>] [--snapshot_root=<path>] [--snapshot_id=<id>] [--snapshot_pinned=<true|false>]
• Description: Generates minimal security fixes using transactional isolation (shadow directories or file backups), applies patches, and verifies them.
• Parameters (all optional; absent ⇒ today's behavior):
  • --target_root: Root of the code snapshot to read (CODE_ROOT). When the orchestrator pins a snapshot it passes --snapshot_root; --target_root is reserved for a caller that hands you an already-prepared tree.
  • --snapshot_root: Root of the pinned immutable snapshot for this pass.
  • --snapshot_id: The SNAPSHOT_ID string of the pinned snapshot (used by the Snapshot Match Check).
  • --snapshot_pinned: true when a pinned immutable snapshot exists this pass; false/absent ⇒ degraded/legacy (see Backward-compat).
  • --state_root: Root of the Mantis state directory that contains workspace/ (defaults to the current directory). ALL workspace/... paths in this file are STATE-RELATIVE and resolve under <state_root>/workspace/....

Input/Output Contract

• Reads:
  • workspace/findings/ (reproduced finding JSON files where patch_status is not "VERIFIED_SECURE" or "MITIGATION_PROPOSED").
  • workspace/.mantis_state.json (to track current loop pass).
  • workspace/.mantis_state.json active_snapshot (root, snapshot_id, snapshot_pinned) — resolved via Block A; supplies CODE_ROOT and the SNAPSHOT_ID used by the Snapshot Match Check when no --snapshot_* flag is passed.
  • Target source code files.
  • Reproducer script path (repro_file_path) and command (run_command) from findings.
  • Pre-existing backup files matching finding ID (if Option B is used).
• Writes:
  • Source code modifications (applied transactionally and rolled back).
  • Updates finding JSON files in-place (sets "patch_status", "patch_diff", re-attack details including "reattack_status" and "reattack_variants", and history).
  • Appends to workspace/learnings.jsonl.
  • Reusable helper script workspace/helpers/append_patch.py.
• Preconditions:
  • Findings must exist in workspace/findings/.
• Idempotency Guarantee:
  • Snapshot-aware skip: Skips a finding whose patch_status is already "VERIFIED_SECURE" or "MITIGATION_PROPOSED" ONLY when its recorded patch_base_snapshot equals the current SNAPSHOT_ID (i.e. it was verified against THIS snapshot). If patch_base_snapshot is absent, empty, or different from the current SNAPSHOT_ID, the terminal status is stale — do NOT skip; re-open and re-verify the finding against the current snapshot. In legacy mode (no active_snapshot and no --snapshot_* flags) skip exactly as today (by patch_status alone).
  • Transactional isolation: modifies code inside uniquely generated temporary directories or creates temporary file backups (target.c.bak-[id]), restoring baseline state upon completion (using try...finally rollback mechanisms).
  • Reuses the existing append_patch.py script once created.

Instructions

Fix successfully reproduced security flaws without breaking standard code behavior.

Execute the patching and verification stage as follows:

0. Snapshot & Locator Resolution (run once, before touching any code):

   0a. Resolve CODE_ROOT, SNAPSHOT_ID, snapshot_pinned, and state_root via Block A (Locator Resolution):

   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).

   For this stage: mantis-patch READS target code (it is NOT a findings-only stage), so it runs Block A steps 1–6 in full. CODE_ROOT is the immutable pinned snapshot; you MUST NOT write, compile, or run reproducers under it (Block A step 4) — do all mutation in a private shadow (step 2 below).

   0b. Determine PATCH_MODE (mechanical, using the resolved values):

   • active_snapshot absent AND no --snapshot_root/--snapshot_id/ --target_root passed ⇒ LEGACY mode (today's behavior; the new ceilings in step 3 do NOT fire).
   • snapshot_pinned == true ⇒ PINNED mode (full gates below apply).
   • snapshot_pinned == false AND SNAPSHOT_ID begins with the literal live: ⇒ HALT/DEGRADED mode (a snapshot was attempted but could not be pinned; authoritative verdicts are forbidden this pass — see step 3).

   0c. For each finding you process, compute its MATCHED/NOT_MATCHED result via Block B (Snapshot Match Check):

   SNAPSHOT MATCH CHECK for finding F (decides MATCHED vs NOT_MATCHED):
   1. If snapshot_pinned is false -> NOT_MATCHED. Stop.
   2. Read F.discovery_commit:
      - missing OR empty OR the literal "MIXED" -> NOT_MATCHED.
      - not exactly equal to SNAPSHOT_ID          -> NOT_MATCHED.
      - exactly equal to SNAPSHOT_ID              -> 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.)
   

   The MATCHED/NOT_MATCHED result is consumed in step 2 (isolation-mode choice) and step 3 (verdict). It never on its own downgrades a verdict in PINNED mode: a NOT_MATCHED finding is RE-verified against the current snapshot via the step-3 gate and, if it passes, is stamped with the current patch_base_snapshot.

1. Load Findings to Patch: Read the JSON files in the workspace/findings/ directory. Filter for findings that are NOT already terminally verified AGAINST THE CURRENT SNAPSHOT — i.e. treat a finding as still-to-process unless its patch_status is "VERIFIED_SECURE" or "MITIGATION_PROPOSED" and its patch_base_snapshot equals the current SNAPSHOT_ID (Snapshot & Locator Resolution step 0). A terminal finding whose patch_base_snapshot is absent/empty/different is STALE — include it for re-verification. (In LEGACY mode, where there is no SNAPSHOT_ID, fall back to filtering on patch_status alone, exactly as before.) Among the included findings, keep those where (either repro_status is "reproduced" OR the finding is an exploit chain, e.g., the title starts with "Exploit Chain:", or history has an entry from the "chainer" stage, or the "constituent_findings" property is present and non-empty). If none exist, notify the user.

2. Generate and Apply Minimal Patches: For each reproduced security flaw:

   • Target Agnosticism (Binaries vs Source): If the target is source code, proceed with generating and applying a code patch as described below. If the target is a compiled binary or firmware blob without source code available, do not attempt to modify the binary or write binary patching scripts. Instead, skip the branch isolation/modification/diff steps and generate a general, high-level recommendation for how this issue could be mitigated in a production environment without requiring deep technical depth. Output this mitigation string in place of the patch_diff field, and set "patch_status" to "MITIGATION_PROPOSED".

   • Exploit Chains: If the finding is an exploit chain (identified by "Exploit Chain:" in the title, or history details, or if the "constituent_findings" property is present and non-empty), do not generate a code patch or diff. Instead, identify its sub-findings by reading the "constituent_findings" array of UUIDs. Monitor the patch status of these constituent findings (listed on disk as workspace/findings/<uuid>.json). Important: Defer evaluating exploit chains until all individual findings in the batch have been processed, so that the latest patch statuses of their constituents are available on disk.

     Evaluate the exploit chain status using these propagation rules (evaluated in order):

     1. Validity Check: Read the validity "status" of each constituent finding. If any constituent's "status" is "FALSE_POSITIVE", update the exploit chain finding's "status" to match it (e.g. "FALSE_POSITIVE") and immediately skip any further patching/verification for the chain. If any constituent's "status" is "DUPLICATE", resolve it to its canonical finding by recursively following its "duplicate_of" property.

        Duplicate Resolution Process:

        1. Locate the Finding File: The finding file for the duplicate (or any parent in the duplicate chain) may have been moved. Search for <uuid>.json in the following locations in order:
           • workspace/findings/<uuid>.json (active findings)
           • workspace/findings/.trash/<uuid>.json (de-duplicated trash)
           • workspace/archive/findings_pass_*/<uuid>.json or workspace/archive/loop*_findings/<uuid>.json (archives from previous passes) If the file cannot be found in any of these locations, treat it as a missing file error.
        2. Cycle Detection: Maintain a set of visited finding UUIDs during the resolution. If you encounter a UUID that has already been visited in the current resolution chain, raise a validation error (cycle detected).
        3. Maximum Depth: Limit the recursion depth to a maximum of 5 steps. If the chain is deeper, abort and report an error.
        4. Extract Status: Once you resolve to the canonical finding (one whose "status" is not "DUPLICATE" or does not have "duplicate_of"), use that canonical finding's "status" and "patch_status" for all downstream checks and propagation. Do not update the exploit chain finding itself to "DUPLICATE".

     2. Missing Files: If any constituent finding's JSON file is missing from the disk, set the chain's "patch_status" to "ERROR".

     3. Constituent Unset or Stale (Pending): A constituent counts as NOT-YET-VERIFIED if EITHER its "patch_status" is unset (null or missing, indicating it has not yet been reproduced/processed) OR its "patch_status" is terminal but its patch_base_snapshot is absent/empty/different from the current SNAPSHOT_ID (verified against a stale snapshot — Snapshot & Locator Resolution step 0). If ANY constituent is NOT-YET-VERIFIED, the chain's "patch_status" must remain unset (null or missing) and you must defer/suspend further evaluation of the chain until that constituent is re-verified on the current snapshot. (In LEGACY mode, where there is no SNAPSHOT_ID, apply only the "unset" half of this rule, exactly as before.)

     4. Constituent Errors: If any constituent's "patch_status" is "ERROR", set the chain's "patch_status" to "ERROR".

     5. Constituent Failures: If any constituent's "patch_status" is "VERIFICATION_FAILED", set the chain's "patch_status" to "VERIFICATION_FAILED".

     6. Successful Propagation: If all constituents have finished verification AGAINST THE CURRENT SNAPSHOT (each is in {"VERIFIED_SECURE", "MITIGATION_PROPOSED", "VERIFICATION_INCOMPLETE"} AND — except in LEGACY mode — each terminal constituent's patch_base_snapshot equals the current SNAPSHOT_ID):

        • If any constituent is "MITIGATION_PROPOSED", set the chain's "patch_status" to "MITIGATION_PROPOSED".
        • If no constituent is "MITIGATION_PROPOSED" and any constituent is "VERIFICATION_INCOMPLETE", set the chain's "patch_status" to "VERIFICATION_INCOMPLETE".
        • If all constituents are "VERIFIED_SECURE", set the chain's "patch_status" to "VERIFIED_SECURE".

     Skip branch isolation, testing, and re-attack steps for the chain finding itself.

   • Optional Parallel Trajectory Search: If your framework supports subagents, you may spawn multiple concurrent subagents to design diverse patch implementations. Test all generated patches that successfully secure the code without breaking standard functionality, and select the best patch (e.g., the most minimal, readable, and idiomatic fix) rather than just the first one that works.

   • Read the original flawed file to grasp function dependencies and structures.

   • Design a minimal, correct patch to mitigate the security flaw (e.g. adding bound checks, validating sizes, inserting NUL-terminators) without breaking other features.

   • Transactional Isolation (VCS-Agnostic & Safe): To ensure safety, reliability, and VCS-agnosticism, do NOT use VCS-based branch operations (such as git branch, git checkout, or git stash).

     You must ensure transactional isolation using a method appropriate for the operating environment. Isolation-method gate (mechanical):

     • If snapshot_pinned is true (PINNED mode) → Option A (Temporary Directory Shadowing) is MANDATORY. Option B and any method that writes under CODE_ROOT are FORBIDDEN (Block A step 4: never write under a pinned snapshot).
     • Else if the finding is a RETRY (it already carries a prior "patch" history entry or a patch_base_snapshot) OR (PINNED mode AND its Snapshot Match Check result is NOT_MATCHED) → Option A is MANDATORY (do not risk editing a live tree that no longer matches the finding). The PINNED mode AND qualifier on the NOT_MATCHED clause is essential: in LEGACY mode (snapshot_pinned=false), Block B returns NOT_MATCHED for every finding as an artifact of no snapshot, not as a signal of drift — so NOT_MATCHED must only fire when it means "the snapshot changed" (PINNED), not when it means "no snapshot exists" (LEGACY).
     • Otherwise (snapshot_pinned is false AND first attempt — no prior "patch" history entry and no patch_base_snapshot) you may choose Option A (recommended), Option B: File-Level Backups, or design/implement Option C: Alternative Isolation (e.g., namespace isolation, container volumes, or local sandboxes) as long as it fully satisfies the invariants below. This covers both LEGACY and HALT mode first-attempt findings (neither has a prior patch to protect, and neither is in the PINNED read-only snapshot regime).

     Whichever method you choose, you must guarantee these invariants:

     1. Zero Workspace Pollution: No backup or intermediate build files left in the original source tree.
     2. Concurrency Safety: Isolation methods must not conflict with other concurrent agents.
     3. Guaranteed Rollback: Wrap all actions in error traps or try...finally blocks to restore the original state on failure.

     • Option A: Temporary Directory Shadowing (Recommended / mandatory when pinned)

       • Warning/Resource constraint: For source trees larger than a few hundred MB, or when many parallel patch workers share the host, and ONLY when NOT in PINNED mode, you may prefer Option B (which touches only the modified files) to avoid exhausting /tmp or memory. In PINNED mode Option B is forbidden regardless of size (the snapshot is read-only); if a full copy will not fit, do not fabricate a verdict — see step 3 HALT handling.

       • Two-root copy: Create a uniquely generated SHADOW_ROOT (e.g. mktemp -d / tempfile.mkdtemp()) OUTSIDE both CODE_ROOT and any /workspace/ path, then copy the relevant source tree FROM CODE_ROOT (the snapshot resolved in Snapshot & Locator Resolution step 0), NOT from an implicit cwd, into SHADOW_ROOT. CODE_ROOT stays untouched and read-only.

       • Perform all edits, compilation, and reproduction testing inside SHADOW_ROOT. Never run a mutating/compiling/reproducing command with cwd = CODE_ROOT (Block A step 4).

     • Critical Guard (Path and Working Directory Safety): You must ensure that every command executed (compilation, testing, verification) runs with its working directory (Cwd) explicitly set to SHADOW_ROOT. If the finding's run_command contains absolute paths under CODE_ROOT (the snapshot) or under the live source root, you must rewrite that prefix to the corresponding path under SHADOW_ROOT before execution.

       Guard Check: When performing path rewriting, only rewrite paths that represent the target codebase files. If a path starts with or contains a /workspace/ segment (where the Mantis state and findings are stored), do NOT replace its prefix (findings/state must remain in the authoritative state_root/workspace/). This separation is unambiguous because a pinned SNAPSHOT_ROOT/CODE_ROOT never contains a /workspace/ segment (guaranteed by the orchestrator's snapshot materialization). Do not execute any modification or verification command against CODE_ROOT or against state_root/workspace/.

     • {TARGET_ROOT} token substitution (MANDATORY before executing any stored command): mantis-reproduce stores run_command/reattack_run_command with the literal token {TARGET_ROOT} for target-tree paths (Step 3 of reproduce), expecting the caller to substitute it. Before executing any stored run_command or reattack_run_command, replace the literal {TARGET_ROOT} token with the tree being executed against:

       • For the Block-G unpatched baseline run: substitute the fresh unpatched CODE_ROOT copy (a fresh mktemp -d copy taken FROM CODE_ROOT).
       • For post-patch verification and attack/reattack runs: substitute SHADOW_ROOT (the patched shadow copy). This substitution MUST happen BEFORE the CODE_ROOT→SHADOW_ROOT prefix rewriting above (the token may expand to a CODE_ROOT path that then needs rewriting for shadow runs). If the literal token survives unsubstituted, the command will fail → evidence absent → forced ERROR (Block F/Block G treat command-not-found / No-such-file as EVIDENCE ABSENT). Never execute a command containing the literal {TARGET_ROOT} token.

     • Generate the unified patch diff by comparing the original source files in CODE_ROOT (the pinned snapshot) with the modified files in SHADOW_ROOT. Use labels so no CODE_ROOT/SHADOW_ROOT absolute prefix leaks into the diff headers.

     • Delete the temporary shadow directory completely when finished.

     • Option B: File-Level Backups (Fallback)

       • Concurrency & Exclusivity Warning: Because Option B modifies files directly in the original workspace, it is concurrency-unsafe when run in parallel with other workspace-modifying agents. Sequential execution must be strictly enforced via locking.
       • Exclusive Workspace Lock: Before performing backups or edits, the agent must acquire an exclusive lock on workspace/.workspace_edit.lock (using fcntl.flock with fcntl.LOCK_EX in Python, or a similar system-level lock). The agent must hold this lock continuously throughout the entire patching, verification, re-attack, and restoration lifecycle for the finding, releasing it only when final baseline files are restored or finalized.
       • Pre-execution Check: Prior to editing, scan the workspace for pre-existing backup files matching the current finding's ID (e.g., *.bak-[current_finding_id]). If found, restore and delete them.
       • Create Backups: For every source file you intend to modify, create a copy with a unique suffix (e.g., cp target.c target.c.bak-[finding_id]).
       • Net-New Files: Track any newly created files to delete them on rollback.
       • Apply Modifications: Edit original target files directly.
       • Generate Unified Diff: Compare backup against modified file using labels to normalize headers (e.g., diff -u --label target.c --label target.c target.c.bak-[finding_id] target.c).

   • 3-Way Patch Rebasing (Phase 2 incremental efficiency): When a prior pass's snapshot and patch are still present on disk (see the reachability check below), the patcher can attempt to REBASE a prior pass's patch onto the current snapshot instead of generating a fresh patch from scratch. This is an optimization for the common case where a prior fix still applies with minor line-number shifts.

     • How: If ALL reachability conditions (a)-(d) below hold, read 3-Way Patch Rebasing with your file-reading tool for the 3-way merge mechanics (base/ours/theirs scratch copies, git merge-file / diff3 invocation, conflict-marker handling). On ANY uncertainty or if the reference cannot be loaded, fall back to fresh patch generation (Phase-1 behavior).
     • When to use (reachability by OBSERVABLE state, not a flag the patcher cannot read): attempt rebasing ONLY when ALL hold: (a) the prior pass's snapshot directory AND the file's prior unpatched version actually EXIST on disk under <state_root>/.mantis_snapshots/ (retention kept them; if the base snapshot was GC'd this fails → fall back); (b) the finding's signature matches an archived finding with a prior patch_diff (same bug, same signature) — this is the ARCHIVED finding referenced by the remaining gates; (c) the ARCHIVED finding's patch_base_snapshot is present and DIFFERENT from the current SNAPSHOT_ID (the snapshot the prior patch was verified against has changed; this is the correct "snapshot changed" test — do NOT test Block B on the CURRENT finding, whose discovery_commit is always == SNAPSHOT_ID in PINNED mode because researcher stamps it, dedupe backfills it, and plan only copy-verbatim's MATCHED findings preserving the original discovery_commit); if the archived finding's patch_base_snapshot is ABSENT or EMPTY (legacy prior pass, or a pre-Phase-2 patcher that did not write it — detected by the helper-version marker at step 6), the snapshot-changed test is UNKN and you MUST fall back to fresh patch generation (do NOT rebase onto a possibly-unchanged base); and (d) the finding's primary file is in changed_files. If signature is absent (legacy finding), condition (b) cannot be satisfied — fall back to fresh patch generation. Do NOT gate on --snapshot_keep: that flag is set on the orchestrator and is NOT passed to or readable by the patch stage; the on-disk presence check (a) is the correct observable substitute and works under any retention setting (the default keep-2 already retains the immediately-prior pass). changed_files and changed_files_status are read from workspace/.mantis_state.json (the same state object read for active_snapshot).

   • When rebasing SUCCEEDS / FAILS / Guardrail: See 3-Way Patch Rebasing for the success (clean merge → use rebased patch, still run Block G, history note patch-rebased-from: pass_<N-1>), failure (merge conflict / file deleted / renamed → fall back to fresh patch generation), and guardrail (on ANY uncertainty, fall back to Phase-1; never apply a rebased patch with unresolved conflicts or unrelated changes).

   • Unpatched-Baseline Re-run in --reattack (Phase 2): When the @mantis-reproduce --reattack sub-agent is re-attacking a patch on a NEW snapshot (Block B NOT_MATCHED, meaning the snapshot changed since the patch was verified — in PINNED mode only), the re-attack MUST first re-establish the unpatched baseline on the CURRENT snapshot before testing the attack against the patched build. This ensures the re-attack is meaningful: if the bug no longer triggers on the current unpatched snapshot (e.g., upstream code fixed it), the re-attack result is inconclusive, not a pass.

     • How: Before running the attack on the patched shadow, run the reproducer against a FRESH UNPATCHED copy of the current snapshot (per Block G step 1). If the unpatched baseline does NOT trigger (evidence absent), set reattack_status = "inconclusive_baseline_changed" with a history note, and do NOT claim failed_to_bypass (the patch was not tested against a live bug). If the unpatched baseline DOES trigger, proceed with the attack on the patched build as normal.
     • HALT-mode note: In HALT mode (snapshot_pinned=false, live: SNAPSHOT_ID), Block B is always NOT_MATCHED, but this does NOT represent a genuine snapshot change — it means the tree couldn't be pinned. The @mantis-reproduce --reattack sub-agent skips the C5 re-baseline in HALT (see reproduce C5 HALT guardrail) and follows the existing HALT ceiling.
     • Guardrail: This does NOT change the VERIFIED_SECURE gate — Block G still requires the unpatched baseline to trigger. This only adds a re-baseline step to the re-attack path when the snapshot changed.

3. Post-Patch Verification Run: (Skip this step for binary-only targets where no code patch was applied). To confirm the patch works, re-run the reproducer script inside your isolated execution environment. Use the exact "repro_file_path" and "run_command" from the reproduction entry to verify the patch.

   • Cwd Enforcement: You must execute the reproducer script with the working directory (Cwd) set to the shadow directory (if using Option A). Ensure the command targets the copy in the shadow directory, not the original workspace.

   • Reached-sink evidence definition — Block F (Reached-Sink Evidence Gate). In patch verification the evidence is required on the UNPATCHED baseline, never on the post-patch attack run (a correct patch legitimately stops the input before the sink):

     REACHED-SINK EVIDENCE GATE (mechanical):
     Each reproducer produces REACHED-SINK EVIDENCE via ONE channel, recorded in repro_hints:
        (a) script/source harness -> write the exact bytes MANTIS_REACHED_ENTRYPOINT to a
            sidecar file $SENTINEL_FILE and flush+fsync (or unbuffered write) BEFORE
            invoking the sink. (A file survives a crash that truncates buffered stdout.)
        (b) binary / firmware / raw-payload -> reached-sink evidence is a captured
            crash backtrace or sanitizer frame (ASan/UBSan/MSan/TSan) that
            explicitly names the target sink function (target-produced tracing). A
            marker written by a wrapper you author BEFORE invoking the target is
            SETUP EVIDENCE ONLY: it proves "launch attempted," not "sink reached,"
            and does NOT qualify as reached-sink evidence. If no in-path marker
            (channel a) and no target-produced backtrace/sanitizer trace
            (channel b) is achievable, the sink is unreached.
      EVIDENCE PRESENT (reached-sink) = (channel a) sidecar file contains
        MANTIS_REACHED_ENTRYPOINT written in-path, OR (channel b) target-produced
        backtrace/sanitizer output names the sink. A wrapper pre-launch marker alone is
        NOT evidence present.
     EVIDENCE ABSENT includes: any compiler/build nonzero exit; exit 127 (command not
       found); exit 2 with a "No such file" message.
     DECISION GATE (gate the DECISION, not specific verdict strings):
       - Record repro_status = reproduced OR statically_confirmed ONLY if EVIDENCE is
         PRESENT. If ABSENT -> repro_status = not_attempted (retry-eligible), STOP.
       - In patch verification, EVIDENCE is required on the UNPATCHED baseline (Block G),
         NOT on the post-patch attack run (a correct patch legitimately stops the input
         before the sink).
       - If NO evidence channel is achievable for this target, downgrade to
         not_attempted / VERIFICATION_INCOMPLETE. NEVER synthesize the marker.
     

   • Hard gate before any VERIFIED_SECURE — Block G (Unpatched-Baseline + Benign-Control Gate). Run it inside SHADOW copies of CODE_ROOT; the "FRESH UNPATCHED copy of SNAPSHOT_ROOT" in Block G step 1 means a fresh copy taken FROM CODE_ROOT:

     UNPATCHED-BASELINE + POST-PATCH GATE (before any VERIFIED_SECURE):
     0. APPLICABILITY: applies ONLY when repro_status == reproduced (a runnable PoC
        exists). If repro_status == statically_confirmed (no runnable PoC),
        VERIFIED_SECURE is NOT applicable -> record MITIGATION_PROPOSED (NEVER ERROR).
     1. UNPATCHED BASELINE: run the reproducer against a FRESH UNPATCHED copy of
        SNAPSHOT_ROOT using Block F. If evidence ABSENT or the bug does NOT trigger ->
        patch_status = ERROR ("reproducer_invalid_on_current_snapshot"); do NOT set
        VERIFIED_SECURE.
     2. POST-PATCH INTEGRITY (distinguish "blocked by patch" from "build break"):
        - REQUIRED: the patched build must COMPILE with exit 0. Nonzero ->
          VERIFICATION_INCOMPLETE.
        - REQUIRED (benign control): run a legitimate BENIGN (non-attack) input through
          the patched build; it MUST reach the sink path (EVIDENCE PRESENT via Block F)
          with no crash. This proves the patch narrowed the bug rather than breaking the
          harness/entrypoint. If NO benign control can be constructed for this target,
          you may NOT claim VERIFIED_SECURE on a clean-run-only basis -> land
          VERIFICATION_INCOMPLETE and record why the benign control was infeasible.
          (Strict mode: a clean compile + clean run WITHOUT a benign control reaching
          the sink is never sufficient for VERIFIED_SECURE.)
     3. ATTACK ON PATCH: run the attack input through the patched build. VERIFIED_SECURE
        requires ALL of: step 1 triggered on unpatched (evidence present), step 2
        integrity holds, step 3 attack does NOT crash/trigger, AND the `--reattack` run
        also fails to bypass. Otherwise VERIFICATION_FAILED.
     

     Sanitizer consistency guardrail (Block G): All runs in this gate (unpatched baseline, benign control, attack, and re-attack) MUST use the SAME sanitizer flags that made the unpatched baseline trigger. If the baseline triggered via UBSan (exit 0, recover-mode), the attack run must also be compiled with UBSan — otherwise the attack might exit 0 without a trace even though the bug is still present, producing a false VERIFIED_SECURE (INV-1 violation). Record the sanitizer flags used in repro_hints so downstream stages replicate them.

   • HALT/DEGRADED ceiling: If PATCH_MODE is HALT/DEGRADED (snapshot_pinned false with a live: SNAPSHOT_ID), authoritative verdicts are forbidden this pass: the best attainable patch_status is "VERIFICATION_INCOMPLETE". Never emit "VERIFIED_SECURE" in this mode. (LEGACY mode is unaffected.)

   • Missing-file rule: If the reproducer file (repro_file_path) or a code_paths target file cannot be found when you attempt verification, set patch_status to "ERROR". NEVER treat a missing file as "did not reproduce" and NEVER emit "VERIFIED_SECURE" from a missing file. (This is also what Block F/Block G's "No such file"/exit 127 → EVIDENCE ABSENT path enforces.)

   • VERIFIED SECURE (all conditions REQUIRED): Mark patch_status as "VERIFIED_SECURE" ONLY if ALL of the following hold:

     1. Block G passes in full: the UNPATCHED baseline triggered the bug WITH reached-sink evidence (Block F) on a fresh copy of CODE_ROOT; the patched build compiled (exit 0); the benign/integrity control held; and the attack input on the patched build does NOT crash/trigger.
     2. Re-attack fails to bypass: a fresh, independent @mantis-reproduce --reattack sub-agent (spawned per the block below) writes reattack_status = "failed_to_bypass" — meaning a non-empty reattack_variants array with ≥ 3 valid variant inputs (reproduce Step 3a) ALL failed to trigger the original vulnerability class on the patched shadow. An empty or short variant set caps at VERIFICATION_INCOMPLETE, never VERIFIED_SECURE.
     3. Not degraded: PATCH_MODE is not HALT/DEGRADED. If PATCH_MODE is HALT/DEGRADED (snapshot mismatch / unpinnable snapshot), the ceiling is "VERIFICATION_INCOMPLETE", never "VERIFIED_SECURE". If Block G reports its baseline could NOT be established (evidence absent or bug does not trigger on the current unpatched snapshot), set patch_status to "ERROR" ("reproducer_invalid_on_current_snapshot") — do NOT emit "VERIFIED_SECURE". If Block G's applicability check found repro_status == statically_confirmed, record "MITIGATION_PROPOSED" (never ERROR). To ensure true independence, launch a fresh @mantis-reproduce --reattack --finding_id=[finding_id] sub-agent against the PATCHED shadow (a copy of SHADOW_ROOT after your patch is applied) to perform the re-attack.

     Important: When calling the @mantis-reproduce subagent for the re-attack:

     • If using Option A (Shadowing) (always, in PINNED mode), pass:
       • --reattack
       • --target_root=<PATCHED_SHADOW_ROOT> — the shadow copy that contains your applied patch. Because --target_root is AUTHORITATIVE and sentinel-EXEMPT (Block A step 1a/2), the sub-agent reads the patched tree directly.
       • --snapshot_pinned=false — the patched shadow is deliberately mutated, so the reproduce sub-agent MUST skip the snapshot sentinel/match check for it.
       • --state_root=<state_root> — your authoritative state directory (so all reattack_* fields and history land under state_root/workspace/).
       • --finding_id=[finding_id] of the finding being verified.
     • If using Option B (Backups) or Option C (Alternative) (only possible in LEGACY mode), pass --reattack, both roots pointing at the live workspace (or leave them default .), and --finding_id=[finding_id].

     The reproducer agent running with --reattack will write its outcomes directly into the primary finding's reattack_status, reattack_file_path, reattack_run_command, and reattack_output fields inside the original workspace findings (state_root/workspace/findings/), keeping the initial repro_* fields untouched.

   • VERIFICATION FAILED: If the sandbox execution still triggers the bug, or if your re-attack successfully bypasses your patch, the patch is insufficient. Re-evaluate and adapt your fix.

   • VERIFICATION INCOMPLETE: If the initial post-patch verification run passed but the subsequent re-attack checks failed/timed out due to sandbox infrastructure errors, environment timeouts, or platform restrictions, set "patch_status" to "VERIFICATION_INCOMPLETE".

   • Re-attack unset / SNAPSHOT_MISMATCH → VERIFICATION_INCOMPLETE: If reattack_status is unset (the re-attack sub-agent left it unset with a SNAPSHOT_MISMATCH or setup_failed history note, or the re-attack did not run at all), set patch_status to "VERIFICATION_INCOMPLETE" — never VERIFIED_SECURE. An unset re-attack status means independence was not confirmed; a SNAPSHOT_MISMATCH means the re-attack ran against a different snapshot than the patch was verified on. In either case the patch is not conclusively verified.

   • Inconclusive baseline → VERIFICATION_INCOMPLETE: If reattack_status is "inconclusive_baseline_changed" (the re-attack sub-agent re-ran the unpatched baseline on the current snapshot and the bug no longer triggers — the baseline changed since the patch was verified), set patch_status to "VERIFICATION_INCOMPLETE" (or "ERROR" with details "reproducer_invalid_on_current_snapshot") — never "VERIFIED_SECURE". The patch was not tested against a live bug on the current snapshot; claiming it is secure would be a false authoritative verdict.

4. Extract Patch and Rollback Transaction: (Skip this step for binary-only targets). Do not leave the codebase in an altered state. Once you have a final outcome (either VERIFIED_SECURE or you have exhausted your retries):

   • If successful, generate a unified diff representing your exact changes and save it to the "patch_diff" field:
     • If using Option A (Shadowing), generate this diff by comparing the original files in CODE_ROOT with the modified files in the shadow directory.
     • If using Option B (Backups), generate this diff by comparing the backup file to the modified file, explicitly labeling the headers to prevent the backup suffix from appearing (e.g., diff -u --label target.c --label target.c target.c.bak-[finding_id] target.c).
     • If using Option C (Alternative), generate a clean, VCS-agnostic unified diff comparing the unmodified baseline files to the final patched files.
     • If multiple files were modified, generate individual unified diffs and concatenate them cleanly into the single "patch_diff" string. Do NOT use VCS-specific diff commands.
   • Transactional Clean Up / Rollback: Restore the codebase to its original state.
     • If using Option A (Shadowing), delete the temporary shadow directory completely (e.g., rm -rf <shadow_directory>). Since the original codebase was never modified, no further restoration is needed.
     • If using Option B (Backups), restore the original files by copying the backup files back onto the target files (e.g., cp target.c.bak-[finding_id] target.c), delete the backup copies (rm target.c.bak-[finding_id]), and delete any net-new files created during the patching process. Do NOT delete any re-attack/PoC script files written inside the workspace/reproducers/ directory, any helper scripts written inside the workspace/helpers/ directory, or the memory database file workspace/learnings.jsonl; these must be explicitly preserved.
     • If using Option C (Alternative), execute the corresponding teardown or rollback steps to fully purge all modification artifacts, delete any temporary resources, and ensure the original workspace is left in its clean baseline state.

5. Append to Long-Term Memory (Continuous Reviewing Link): For each security flaw processed, append a single structured JSON line to a workspace database file named workspace/learnings.jsonl (using append mode). This allows the strategist (/mantis-plan) to read these historical records in subsequent passes and avoid proposing fixes for already patched files.

   • Memory Entry Format: {"title": "[security_flaw_title]", "code_paths": ["[path1:line1]"], "status": "[VERIFIED_SECURE / MITIGATION_PROPOSED / VERIFICATION_INCOMPLETE / VERIFICATION_FAILED / ERROR]", "patch_base_snapshot": "[current SNAPSHOT_ID, or omit in LEGACY mode]", "snapshot": "[current SNAPSHOT_ID, or omit in MODE-OFF]"}

6. Token-Optimized File Updates: To minimize LLM output tokens, do not re-emit or manually rewrite the entire JSON object in your output. Instead, write a reusable helper script (e.g., state_root/workspace/helpers/append_patch.py) during your first finding update. Make the FIRST line of the helper a version marker comment: # MANTIS_HELPER_VERSION = 2. Before reusing an existing helper, read its first line: if it does NOT contain the exact marker MANTIS_HELPER_VERSION = 2, the helper is stale (from an older pass/version that does not write patch_base_snapshot) — regenerate it. Only when the marker matches may you reuse it: simply execute the existing helper with the new parameters to append the required fields.

   You must append the following to the existing object:

   • A "patch_status" field (one of "VERIFIED_SECURE", "MITIGATION_PROPOSED", "VERIFICATION_INCOMPLETE", "VERIFICATION_FAILED", or "ERROR").
   • A "patch_base_snapshot" field set to the current SNAPSHOT_ID (Snapshot & Locator Resolution step 0) — the snapshot this verdict was earned on. Omit this field only in LEGACY mode (no SNAPSHOT_ID exists). This is what makes the snapshot-aware skip (Idempotency Guarantee) and chain propagation correct across passes.
   • If a patch was successful, a "patch_diff" field containing the unified diff.
   • If a re-attack was performed, the "reattack_status", "reattack_file_path", "reattack_run_command", "reattack_output", and "reattack_variants" fields (each object in "reattack_variants" MUST have EXACTLY {"description": "...", "triggered": true/false}).
   • An entry to the "history" array:

   {
     "stage": "patch",
     "action": "patched",
      "details": "Patch status evaluated as [VERIFIED_SECURE/MITIGATION_PROPOSED/VERIFICATION_INCOMPLETE/VERIFICATION_FAILED/ERROR] on snapshot [patch_base_snapshot or 'legacy']",
     "pass_number": <current_pass_number>,
     "timestamp": "<current_iso8601_timestamp>"
   }
   

When complete, notify the user.