Architect (/mantis-architecture)

System Goal

Knowledge Base Synthesizer. Translates ephemeral insights from the learnings queue (workspace/learnings.jsonl) and structural analysis of the codebase into a canonical, interlinked Markdown Knowledge Base (workspace/kb/).

Command Definition

Command: /mantis-architecture
Description: Builds the foundation of the KB by defining system architecture, mapping specific entities (components), and categorizing historical vulnerability patterns.
Arguments (all optional; resolved by LOCATOR RESOLUTION / Block A): --snapshot_root=<dir> (or the SNAPSHOT_ROOT env var) — the pinned code snapshot to read target source from; --snapshot_id=<id> — the SNAPSHOT_ID of that snapshot; --state_root=<dir> — the parent of workspace/ for all state and KB paths; --target_root=<dir> — an already-prepared tree that OVERRIDES the snapshot (rarely passed to this stage). When none are passed, behavior is byte-for-byte today's (degraded/unpinned): read source from the current directory and treat snapshot_pinned as false.

Input/Output Contract

Reads:
- workspace/learnings.jsonl (raw insights from the current round).
- workspace/historical_learnings.jsonl (optional, past vulnerability metadata).
- Codebase directory structure and key source files.
- Existing Markdown files in workspace/kb/ (to validate/decay check).
- workspace/.mantis_state.json (to retrieve pass count).
- workspace/.mantis_state.json → active_snapshot (root, snapshot_id, snapshot_pinned) and snapshot_history — provenance for the KB freshness gate (step 0b). Read the snapshot from STATE ONLY; NEVER run a live VCS command (git/hg/repo) to decide KB currency.
- workspace/.mantis_state.json → kb_snapshot_id (the SNAPSHOT_ID the current KB was last built against; absent on a first/legacy KB).
- workspace/.mantis_state.json → changed_files and changed_files_status (written by mantis-plan's Block E; consumed by the scoped KB invalidation in step 0b outcome 3. Present from pass 2 on, but may be stale (written in a prior pass) — the scoped path checks changed_files_pass against state.pass_number and falls back to full rebuild if they differ.)
Writes:
- Markdown files under workspace/kb/ (architecture.md, entities/[component_name].md, vulnerabilities/[CWE-ID].md, index.md).
- workspace/kb/dependencies.json — a JSON map of import/dependency edges extracted during architectural analysis (keys = source file paths relative to CODE_ROOT; values = arrays of files that import/depend on the key file). This is consumed by mantis-plan's dependency-aware fan-out (Phase 2). If the codebase has no parseable import structure, write {}. Re-derive only changed entries during scoped invalidation (see outcome 3 below).
- Archives workspace/learnings.jsonl to workspace/archive/learnings/learnings_pass_${N}_${X}.jsonl.
- A  marker as the FIRST line of every (re)written KB file (index.md, each entities/*.md, each vulnerabilities/*.md), plus kb_snapshot_id = SNAPSHOT_ID in workspace/.mantis_state.json.
- An immutable per-pass copy of the whole KB tree to workspace/archive/kb/kb_pass_${N}_${X}/ (so a later reverted fix cannot silently erase the record of what the KB claimed at pass N).
Preconditions:
- workspace/learnings.jsonl must exist.
Idempotency Guarantee:
- Transactional: moves workspace/learnings.jsonl to archive only after programmatically verifying all KB Markdown updates were written successfully. KB files are overwritten in-place.
- Snapshot stamping is part of the same transaction: the KB_SNAPSHOT markers, the per-pass workspace/archive/kb/kb_pass_${N}_${X_kb}/ copy, and the kb_snapshot_id state write complete before (or together with) the learnings move. On any failure, leave workspace/learnings.jsonl intact.

Instructions

Analyze the codebase and pending learnings to construct a permanent, Markdown-based memory for future agents.

Execute the architecture stage as follows:

LOCATOR RESOLUTION (Block A, inlined below):

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.

This is a CODE-READING stage (steps 2 and 4 read target source), so Block A steps 1-6 all apply; it is NOT findings-only. Resolve CODE_ROOT, SNAPSHOT_ID, and snapshot_pinned from state BEFORE doing anything below. Per Block A step 3, all workspace/kb/... paths are STATE-RELATIVE: read and write them under state_root/workspace, NEVER under CODE_ROOT. Read all target source under CODE_ROOT. Do NOT run any VCS command to decide KB freshness (Block A step 5's carve-out is only for history/diff/blame, which this stage does not use).

0b. KB SNAPSHOT FRESHNESS GATE (mechanical; STATE + KB marker only, NO live VCS):

- `CUR` = `SNAPSHOT_ID` (resolved by Block A; the empty string if
  `active_snapshot` was absent). `PINNED` = `snapshot_pinned` (false if absent).
- **MODE-OFF short-circuit (3-state rule):** if `active_snapshot` is ABSENT
  in state (no `--sync` was requested — MODE-OFF = today's default), SKIP the
  freshness gate entirely: do a best-effort build/update against `CODE_ROOT`,
  do NOT prepend any STALE banner, and do
  NOT stamp `kb_snapshot_id`. This is byte-for-byte today's behavior. (Only
  HALT and PINNED run the gate below.)
- `KB_ID` = the `kb_snapshot_id` value in `.mantis_state.json` (primary); else the
  text after `KB_SNAPSHOT:` on the FIRST line of
  `state_root/workspace/kb/index.md` if that file exists (secondary fallback,
  for legacy runs without state); else `""` (no prior KB). State is primary so
  the file-marker parsing pitfall (comment-wrapped first line, no `-->`
  stripping) can never strand `KB_ID` with the comment closer and force BUILD
  FRESH every pass.
- Choose EXACTLY ONE outcome by string checks, top to bottom, first match wins:
  1. `PINNED` is false (HALT mode — `active_snapshot` present but unpinned)
     ->  **STALE / HALT.** Do a best-effort build/update against `CODE_ROOT`,
     but PREPEND the STALE banner (below) as the first lines of `index.md`.
     Do NOT claim currency: leave the
     banner in place. Set `kb_snapshot_id` = `CUR` (a `live:` id).
  2. Else `KB_ID` == `CUR` (both non-empty)  ->  **CURRENT.** Do the incremental
     update + decay-check (step 4) as today. Re-stamp `KB_SNAPSHOT: CUR` on
     every (re)written file. REMOVE any STALE banner previously prepended to
     `index.md`.
  3. Else (`PINNED` true AND (`KB_ID` is empty OR `KB_ID` != `CUR`)) ->
     **BUILD FRESH (full or scoped re-architecture).** The pinned code advanced
     since the KB was built (a sync / pass-boundary change), OR the KB is
     unstamped / legacy. Choose full or scoped:
     - **Scoped invalidation (Phase 2 incremental efficiency):** If
       `changed_files_status` is known (not UNKNOWN) AND the KB already has a
       `KB_SNAPSHOT` stamp (KB_ID was non-empty, just different) AND
       `changed_files_pass` equals the current `state.pass_number` (the diff
       is from THIS pass, not a stale prior pass — absent or different →
       treat as UNKNOWN → full rebuild below), attempt a SCOPED rebuild: only
       invalidate KB entries whose source files are in `changed_files`, plus
       their parent-rollup dependents (KB entities that import/reference the
       changed files). Re-derive ONLY those entries from `CODE_ROOT`; carry
       forward all other KB entries unchanged (they were built against the
       same code, just a different snapshot ID). Re-stamp `KB_SNAPSHOT: CUR`
       on every (re)written file.
        - **Parent-rollup (2-hop, matching plan's fan-out):** When
          invalidating a KB entry for changed file F, also invalidate any KB
          entry that REFERENCES F directly (1-hop) AND any entry that
          references a 1-hop dependent of F (2-hop). This matches
          `mantis-plan`'s dependency-aware fan-out (which expands up to 2
          hops), ensuring that a grandchild entity (H imports G, G imports
          changed F) is not carried forward stale and later fed as a
          `kb_reference` while its dependency has changed.
       - **Guardrail:** If ANY uncertainty arises (can't determine which KB
         entries map to which source files, the KB structure is ambiguous, or
         changed_files is empty but KB_ID != CUR), fall back to full rebuild
         below. Never carry forward a stale entry for a changed file.
     - **Full rebuild (Phase-1 fallback):** If KB_ID is empty (no prior KB),
       OR `changed_files_status` is UNKNOWN, OR the scoped invalidation guardrail
       fired, REBUILD every KB file from scratch against `CODE_ROOT`. Do NOT
       carry forward any prior assertion you have not re-derived from
       `CODE_ROOT` this pass. Stamp `KB_SNAPSHOT: CUR`. REMOVE any STALE banner.
- STALE banner (paste verbatim, substituting `<KB_ID>` and `<CUR>`; keep the
  leading `>` on every line so it renders as a visible blockquote):

  ```
  > **STALE KB WARNING — do not trust without re-verifying.**
  > snapshot_pinned=false, or the KB was built against a different snapshot.
  > KB_SNAPSHOT=<KB_ID> does not match active_snapshot.snapshot_id=<CUR>.
  > Every SECURE/FIXED/NON_VIABLE/SAMPLE_OR_TEST claim below is UNVERIFIED
  > against the current code. Re-verify before trusting; do NOT filter, skip,
  > or down-prioritize work based on this KB.
  ```

Read the Inbox (workspace/learnings.jsonl and workspace/historical_learnings.jsonl):
- Parse the contents of workspace/learnings.jsonl (and workspace/historical_learnings.jsonl if it exists). Extract all trajectory insights, discovered vulnerabilities, viable crash paths, and verified patches.
Analyze Source Code Boundaries:
- Examine the directory structure and key source files under CODE_ROOT (the pinned snapshot resolved by Block A; use absolute paths per Block A step 6, and do NOT run a VCS command). Dynamically identify the core components, interfaces, and trust boundaries of the system based on the repository's contents. This applies broadly across domains: whether it is a software system (e.g., identifying parsers, controllers, or network daemons), a hardware/RTL design (e.g., identifying IP blocks, JTAG interfaces, or memory controllers), Infrastructure-as-Code (e.g., identifying cloud permissions, VPC perimeters, or deployment descriptors), or data/ML pipelines (e.g., identifying data ingress points, model serialization mechanisms, or training boundaries).
Build or Update the Knowledge Base (KB):
- Create or update files in the workspace/kb/ directory using standard Markdown. Follow these strict paths:
  - workspace/kb/architecture.md: High-level data flows, zone definitions, system design, and overall availability/uptime requirements (if documented or inferable from configuration like systemd, kubernetes, or load balancers).
  - workspace/kb/entities/[component_name].md: Specific definitions for components (e.g., auth_module.md). Must include links to associated vulnerability classes and document known constraints (e.g., "This module sanitizes input X"). Document the component's criticality and availability requirements (classify as CRITICAL, STANDARD, or LOW_CRITICALITY if applicable). Incorporate trajectory insights here.
  - workspace/kb/vulnerabilities/[CWE-ID_or_BugClass].md: Descriptions of bug classes (e.g., CWE-79.md or Memory-Corruption.md) that have been historically relevant to this codebase, including examples of what not to do.
  - workspace/kb/index.md: A root catalog containing links and 1-line summaries to every file created above. This is the map the Planner will read.
- Important Formatting Rules: Use relative links to cross-reference entities and vulnerabilities (e.g., [Auth Module](entities/auth_module.md)). Ensure all markdown files are concise and focused on actionable security context.
- Snapshot stamping (REQUIRED on every (re)written KB file when running the freshness gate, i.e. HALT or PINNED; never in MODE-OFF): Make the FIRST line of index.md, each entities/*.md, and each vulnerabilities/*.md exactly  (substitute CUR from step 0b; it is an HTML comment so it does not render). This is how the next pass's freshness gate (step 0b) detects drift. MODE-OFF gate (3-state rule): if active_snapshot is ABSENT (MODE-OFF — no --sync was requested), do NOT stamp the per-file KB_SNAPSHOT marker: CUR is the empty string (arch:145: "the empty string if active_snapshot was absent"), so the mandated marker would be  (empty value) — a snapshot-era artifact that did not exist in Phase 1. The per-file marker is ONLY consumed by step 0b's freshness gate, which MODE-OFF skips entirely (arch:147-152: "SKIP the freshness gate entirely... This is byte-for-byte today's behavior. Only HALT and PINNED run the gate below."). This MODE-OFF gate mirrors the freshness gate logic below and step 0b's outcome clauses, which mention per-file KB_SNAPSHOT: CUR stamping only in HALT/PINNED outcomes (CURRENT :164, scoped BUILD FRESH :178, full BUILD FRESH :195).
- Per-file KB_SNAPSHOT stamping is the sole provenance mechanism for KB assertions. Do NOT write per-assertion (AS_OF:<snapshot>) tags — the AS_OF re-verification reader was never built, and staleness protection is already provided by the freshness gate (step 0b) comparing kb_snapshot_id to SNAPSHOT_ID, plus per-finding discovery_commit (enforced by mantis-critic Block B). A later-reverted fix is caught by these mechanisms, not by per-assertion tags.
Validate and Decay Knowledge (Drift Prevention):
- Knowledge becomes stale when code is patched or refactored. Before finalizing the KB updates, spot-check the assertions in the existing workspace/kb/entities/ against the source under CODE_ROOT (the pinned snapshot — NOT a live VCS query, and NOT the live working tree). In the BUILD FRESH outcome (step 0b) do NOT spot-check at all: discard the prior assertions and re-derive every entity from CODE_ROOT this pass. In the STALE / HALT outcome, spot-check only best-effort and keep the STALE banner regardless of the result.
- If an entity file claims a variable is un-sanitized (based on an old learning) but the live code now contains a sanitization function (because a patch landed), delete or correct that outdated learning in the KB.
- If a learning is repeatedly proven wrong by the current trajectory insights, actively correct it to prevent the "wrong learning" from persisting and blinding future agents.
- When you correct or re-confirm a finding-derived assertion, re-stamp the KB_SNAPSHOT marker on that KB file.
Transactional Inbox Clearing & Archiving:
- To prevent infinite loops and token bloat, you must clear the queue and archive the learnings.
- Verify and Finalize: Programmatically verify that all Markdown KB updates were successfully written to disk and that cross-references are valid. Also verify, before committing, that every (re)written KB file BEGINS with its  marker and that every finding-derived verdict is grounded in the current SNAPSHOT_ID.
- Commit by Moving: Only after verifying synthesis success, move workspace/learnings.jsonl to the archive directory:
  - Ensure the target directory exists (e.g., mkdir -p workspace/archive/learnings/).
  - Determine the loop pass number N by reading "pass_number" from workspace/.mantis_state.json. If missing or invalid, scan workspace/archive/ for folders matching findings_pass_N or loopN_findings and resolve N to max_found + 1, defaulting to 1 if no archives exist.
  - Determine the sub-index X by counting existing files matching learnings_pass_${N}_*.jsonl in workspace/archive/learnings/ and adding 1.
  - Move the file: mv workspace/learnings.jsonl workspace/archive/learnings/learnings_pass_${N}_${X}.jsonl.
- Snapshot the KB (per-pass archive): After a successful synthesis, copy the whole KB tree to a per-pass archive:
  - Ensure the directory exists (mkdir -p workspace/archive/kb/).
  - Compute sub-index X_kb = (count of existing kb_pass_${N}_* directories in workspace/archive/kb/) + 1.
  - Copy (do NOT move — the live workspace/kb/ must persist for the next pass): cp -a workspace/kb/. workspace/archive/kb/kb_pass_${N}_${X_kb}/.
- Stamp state: Write kb_snapshot_id = SNAPSHOT_ID (CUR from step 0b) into workspace/.mantis_state.json. If active_snapshot was absent (MODE-OFF), do NOT write kb_snapshot_id and do NOT prepend any STALE banner (the freshness gate was skipped). In HALT mode, write kb_snapshot_id = CUR and leave the STALE banner in index.md.
- If synthesis fails or is interrupted, leave workspace/learnings.jsonl intact in its original location to ensure no data is lost.
- If workspace/learnings.jsonl is ABSENT on entry (e.g. the Stage-15 invocation, because the Stage-2 invocation already archived it this pass), skip ONLY the learnings move; STILL run the freshness gate (step 0b), stamp the KB_SNAPSHOT markers, write kb_snapshot_id, and copy the per-pass KB archive. KB provenance must be recorded on every invocation.

When complete, notify the user.