DocForge2/DEVELOPMENT_NOTES.md

# DocForge2 development notes

This is the running implementation record for DocForge2. It records what is active, what was
measured, what changed, what failed, why architectural decisions were made, and which ideas were
deferred. Stable user and compatibility contracts still belong in dedicated documentation.

## Working rules

- Only one milestone is active at a time.
- `main` remains the last fully verified milestone.
- Active implementation occurs on `dev`.
- Every milestone begins from direct repository evidence and ends with focused tests, the complete
  repository gate, updated measurements, documentation closeout, and a clean pushed state.
- WorldForge, ScrapeStation, legacy DocForge, and production MCP bindings remain out of scope.
- DocForge2 does not self-host during this program.
- Release tags and Forgejo releases require Rob's explicit approval.

## Milestone 0 — complete

Milestone 0 established the public successor, preserved the complete lineage and v1 tag, integrated
the no-AST and adapter-lifecycle work, froze compatibility guarantees, added repository-native
quality and contract gates, and recorded cold/warm performance, memory, rendering, and response
sizes.

The central measurement was decisive: a 1,000-node warm exact lookup took about 286 ms while the
generation-pinned SQLite query path took about 0.4–1.4 ms. Repeated whole-source loading and
validation, not SQLite, is the first optimization target.

## Milestone 1 — complete: fast, observable core

### Outcome

Warm retrieval should disappear into normal tool overhead. Routine reads must not parse project
sources. Status must not render or rebuild hidden work. Results must remain bounded independently
of project size.

### Starting evidence

- Generic `Project.load()` walks, captures, parses, rereads, validates, hashes, and checks Git for
  the complete source set.
- Exact retrieval validates twice around one bounded SQLite query.
- Context compilation performs three full project loads.
- Render status recompiles the complete manual.
- Incremental adapters already prove that manifest attestation can make no-change synchronization
  and exact retrieval sub-millisecond on a tiny fixture.
- Pinned viewer queries prove the current SQLite schema can serve bounded reads quickly.

### Final outcome

Routine generic reads now parse zero canonical source files, use one generation-pinned SQLite
snapshot, and return bounded results. Status checks perform no hidden rendering or rebuilding.
Structured counters prove those invariants independently of machine timing. Complete loading and
deep validation remain recovery and equivalence oracles.

### Work log

#### Linear dependency validation

The inherited dependency-cycle preparation scanned every edge once for every node. The graph
validator now constructs dependency adjacency in one edge pass and sorts each adjacency list before
an iterative deterministic depth-first cycle check. The iterative stack also removes recursion
depth as a failure mode on large valid graphs. The same edge pass now rejects missing sources as
well as missing targets.

A 10,000-node regression test counts complete edge-collection iteration passes and caps them at
four. The focused correctness and bounded-pass tests pass, and the configured strict source type
gate is clean.

One validation command initially included `tests/test_core.py` in a direct Pyright invocation.
Repository Pyright intentionally covers `src` and `tools`, so that command reported existing
untyped test-result indexing rather than a source defect. Rerunning the repository-configured type
gate produced zero diagnostics.

#### Persistent generic source generations

Generic projects now persist a version-1 source-generation receipt only after complete source
loading and fully verified index publication. The receipt binds the explicit generic source
contract, project and root identity, adapter, revision, source hash, every canonical/authority/
descriptor regular-file identity, and every source-membership directory identity.

A normal warm check reads no canonical source bytes. It validates the known directories and files
directly using device, inode, mode, size, nanosecond modification time, and nanosecond change time.
Directory identities detect add, delete, and rename operations without an `rglob`. Any missing,
malformed, incompatible, foreign, or dirty receipt becomes a cache miss and falls back to the full
canonical load and row-verification oracle. Successful fallback verification repairs the disposable
receipt.

The final 1,000-node evidence run initially exposed a repeatable 52 ms exact-read maximum against
the 50 ms target. Profiling showed no source parsing or SQLite cost; each request rebuilt and
revalidated 1,000 `Path` objects from the unchanged JSON receipt twice. The project binding now
caches only the strictly validated receipt structure behind its device, inode, size, modification
time, and change-time signature. Canonical file and directory identities are still recaptured
before and after every query. Receipt replacement or mutation invalidates the cache and fails
closed. The same ordered exact-read profile fell from about 40–52 ms to about 18 ms without
weakening stale-read refusal.

The receipt is deliberately generic-project behavior. Incremental adapter manifests retain
authority over generated or specialist source identities. A one-method legacy adapter continues to
work even when it cannot provide a cheap generation.

#### Request-scoped immutable reads

Index reads now use one read-only SQLite transaction pinned to one verified file signature and one
source identity. Existence checks and queries share that connection. Before returning, the request
rechecks the index signature and current cheap source generation. A concurrent source or index
change fails closed.

Context compilation hydrates nodes and edges from the pinned derived snapshot while retaining
profiles from the immutable descriptor. It no longer loads or parses canonical sources. The public
full `Project.load()` and deep `ProjectIndex.check()` behavior remains the recovery and equivalence
oracle.

Focused tests prove that fresh-process-style generic reads can run exact, search, filter,
backlinks, dependency, impact, context, and no-change synchronization operations while
`Project.load()` is forbidden. They also prove a final source-generation change is rejected before
return and missing/corrupt receipts fall back and repair.

The final clean 1,000-file run recorded:

| Operation | Milestone 0 median | Milestone 1 median | Milestone 1 p95 |
|---|---:|---:|---:|
| Warm no-change synchronize | 142.479 ms | 9.192 ms | 9.324 ms |
| Exact node | 286.306 ms | 17.887 ms | 18.577 ms |
| Search, limit 20 | 288.793 ms | 19.518 ms | 19.884 ms |
| Dependencies, depth 8 | 287.791 ms | 18.117 ms | 19.061 ms |
| Context, 32k, page 20 | 436.897 ms | 25.395 ms | 25.867 ms |
| Render status | 150.591 ms | 18.969 ms | 19.613 ms |
| Visualization status | — | 9.875 ms | 10.836 ms |

The recorded run came from clean commit `6253c45a5eca01efa8c73ea3dfe4d85c55878ada`.
Every measured operation passed its p95 threshold and work-counter contract.

#### Read-only audit reconciliation

The three Milestone 1 audits agreed on the main architecture:

- Keep complete loading and deep checking as independent truth oracles.
- Trust only versioned, identity-bound disposable generation receipts.
- Use one pinned read transaction and retain a final dirty check.
- Hydrate context from the current index.
- Replace full-edge traversal scans with bounded indexed frontier reads.
- Add compact success receipts before allowing large mutations to report post-write size errors.
- Replace hidden render-status rendering with a receipt comparison.
- Add algorithmic counters and parse-count gates alongside wall-clock thresholds.

One audit identified a correctness risk beyond latency: a large mutating MCP operation can commit
successfully and then be replaced by `result_too_large`. This must be fixed in Milestone 1 so
exactly-once operations never report a false failure after mutation.

#### Mutation success receipts

Proposal, preview, and canonical-application MCP mutations now declare an internal response policy.
Before runtime validation or mutation, the service proves that a minimum receipt containing the
actual input identity and fixed-length hash fields fits the configured output limit. If it cannot,
the operation returns a preflight size error with `mutation_committed = false` and does not call the
mutation.

Small results retain the existing full payload. Oversized successful results become a version-1
compact receipt that preserves exact changeset identity, hash, workflow scalars, and lifecycle
state while omitting full operations. Application receipts also preserve changed-source counts and
derived-refresh status/counts. If the compact form is still too large, the service returns the
minimum receipt proven by preflight. It never converts committed success into a post-write size
failure.

End-to-end MCP tests exercise two large hash-chained appends followed by canonical application.
Each response stays within 1,600 compact JSON characters, exposes the new exact hash, and reports
committed success. A separate 700-character preflight test proves the callback and changeset file
are never created. Changeset lifecycle receipts now obey the configured changeset byte limit on
both write and read.

#### Receipt-based render status

Successful declared renders now publish a bounded, atomic version-1 receipt below the disposable
cache. It binds project/root/adapter/source identity, the normalized view configuration, renderer
identity, template and output hashes, byte size, and safe regular-file identities. Generic renders
also publish the verified source generation used by cheap status.

Normal status compares only source-generation, descriptor/view, template-file, output-file, and
receipt identities. It does not call `Project.load()`, prepare the renderer, construct HTML, read
the full output, rebuild the index, or repair missing state. Missing and corrupt receipts are
`unverified`; source, template, or output changes are `stale`. An explicit `deep` option on the
Python, CLI, and MCP status surfaces preserves the old side-effect-free full-render equivalence
oracle.

Receipt failure after atomic output replacement is reported as degraded publication success, not a
false render failure. Canonical application converts the same condition into a degraded
derived-refresh report while retaining canonical success. Focused tests forbid source loading and
renderer preparation during warm status and cover output, template, missing-receipt, corrupt-
receipt, and post-publication receipt-failure behavior.

After race hardening, a 50-sample three-node receipt-status check measured a 3.202 ms median and
3.509 ms p95, compared with the 1.941 ms Milestone 0 three-node full-render status. The small
fixture does not show the scaling benefit; the 1,000-node Milestone 0 status baseline was
150.591 ms and will be rerun in the final Milestone 1 evidence pass.

#### Bounded indexed retrieval

Search, metadata filtering, backlinks, dependency traversal, and impact traversal now query one
extra row beyond the requested bound and report `limit` plus `truncated`. Backlinks, dependency,
and impact APIs accept the same additive `limit` option through Python, CLI, and MCP surfaces.
Omitted limits are capped by the project `max_results` policy.

Traversal no longer loads the complete edge table and repeatedly scans it. It performs
deterministically ordered frontier queries through the existing source primary key or target index.
Each request also has a deterministic edge-examination budget derived from its result limit. The
response includes `candidate_edges_consumed`, `candidate_edges_limit`, and `truncation_reason`
counters so algorithmic work can be asserted independently of machine timing. `truncated` is true
when either another unique result exists or the work budget prevents proving completeness.

The read-only query-plan audit found that source-ordered unfiltered incoming traversal required a
temporary SQLite sort with the version-2 `(target_id, relation, source_id)` index. Direct
`EXPLAIN QUERY PLAN` evidence showed `USE TEMP B-TREE FOR ORDER BY`. A measured additive
`(target_id, source_id, relation)` index removes that sort. The disposable index schema is now
version 3, so existing version-2 indexes rebuild without changing canonical source or proposals.
Frontier cursors are streamed and stop immediately on the first omitted unique result. A focused
core, CLI, MCP, Ruff, and Pyright gate passes for this work-in-progress slice.

#### Structured profiling and zero-work gates

DocForge now has an opt-in, request-local diagnostics collector backed by `ContextVar`. It emits
one bounded version-1 aggregate with a fixed operation name, outcome, total elapsed nanoseconds,
fixed stage timing keys, and fixed integer counters. It never records paths, node IDs, queries,
source text, or SQL. Disabled mode reads no clock and adds no response field, preserving the
existing CLI and MCP payloads.

The generic loader, adapter projection and extraction paths, source-generation checks, index
checks/synchronization/build/read transactions, render status/preparation/output hashing, MCP
runtime validation, and viewer-manager requests now expose direct proof counters. A warm
incremental adapter cache hit still counts the enclosing project load, so the counters cannot hide
full adapter assembly merely because extraction was reused.

MCP servers and the CLI accept the additive `--diagnostics` startup option. Diagnostics are
attached to structured successes and errors only when the complete MCP response still fits its
configured output budget; they are discarded before any primary result or compact mutation
receipt. Warm generic error decoration now reads the persisted source generation before falling
back to complete loading. Render- and visualization-status error paths explicitly disable both
recovery synchronization and complete identity loading.

Context isolation tests cover threads, concurrent async tasks, repeated stages, nested collectors,
exceptions, and disabled collection. Repository tests assert that warm success and error reads,
render status, and visualization status perform zero project loads, source parses, adapter
projection/extraction, index builds, render preparation, output construction, and output hashing.
The result JSON schema contains the same closed operation, stage, and counter sets as the
implementation.

The maintained `tools/milestone1_benchmark.py` harness adds hard counter and p95 latency gates to a
disposable generic project. The smoke target is part of `make gate`; the final 1,000-node evidence
is recorded in `benchmarks/milestone1-2026-07-29.json`. The historical Milestone 0 harness remains
behaviorally unchanged as comparison evidence; it only exposes shared fixture and measurement
helpers to the Milestone 1 harness.

#### Visualization snapshot freshness

Visualization workers now receive a version-1 snapshot specification containing the exact
validated index publication signature: device, inode, size, modification time, and change time.
Both the manager and worker reject a launch if that publication changes before startup. The
transmitted project root, root fingerprint, source identity, adapter, counts, limits, and confined
index path are strictly validated before the worker may serve source or graph data.

Worker health reports index freshness through stat-only comparison. It does not open SQLite and
does not renew the browser activity lease. The version-2 viewer-manager protocol validates the
complete worker identity and distinguishes an unreachable worker from a live stale worker. A stale
worker stays lifecycle `running` for accurate diagnosis, but the next visualize request stops it
and launches a newly validated snapshot instead of reusing it.

Client status separately compares the worker's pinned source identity with
`IncrementalStateProject.incremental_state()`. The composite snapshot is stale if either proof is
stale, current only when both proofs are current, and unknown otherwise. A stopped worker has
unknown snapshot identity. MCP preserves this state at the top-level `staleness` field and disables
recovery synchronization and full-load error decoration.

Tests cover signature mutation before worker startup, malformed identity, missing and symlinked
indexes, stat-only health, unchanged activity, current/unknown/stale source states, live stale
workers, non-reuse, and zero-load status. The Milestone 1 benchmark now measures current, stale,
not-running, and unavailable visualization status separately with the same zero-work and 50 ms p95
gates as other receipt status operations.

#### Bounded pagination and exact large-result review

The final Milestone 1 contract audit found that count limits and the global MCP output ceiling were
not sufficient. A 1,000-node context response already exceeded the normal 200,000-character tool
limit, and one allowed changeset operation can be larger than that limit. Returning
`result_too_large` kept transport bounded but stranded useful evidence.

Version-1 pagination now uses canonical, base64url cursors with a domain-separated SHA-256
corruption checksum. Cursors bind the project, adapter, canonical generation, semantic query,
collection hash, and position. They are deliberately unkeyed read tokens rather than authorization
credentials. Corrupt tokens fail as `invalid_cursor`; changed generations or collections fail as
`stale_cursor` with explicit pagination-restart remediation.

Context transport flattens the compiler's deterministic selected entries followed by all explicit
omissions, then partitions each page back into the existing arrays. Both item count and exact
compact-JSON response size constrain packing. An individually oversized entry becomes a bounded,
hash-identified omission and advances the cursor, avoiding an infinite retry while preserving the
fact that evidence was excluded.

Changeset list, inspection, validation, and diff reads preserve direct full-result defaults while
MCP uses bounded pages. Pages retain exact changeset identity and hash. Large operation pages
compact content-bearing fields into hashes and character counts. A single oversized structured
diff is serialized once as canonical ASCII JSON and returned through hash-bound chunks that
reconstruct the exact legacy `operations` and `changes` arrays. This solves transport growth
without lowering canonical changeset limits or adding cursor storage.

The benchmark now validates zero-work and operation-specific counters for every warmup and measured
sample, records bounded semantic response summaries, covers filter, backlinks, outgoing and
incoming traversal, and measures current/stale/missing/corrupt render receipts plus all
visualization lifecycle states. A maintained query-plan test prevents the incoming traversal
temporary sort from returning.

#### Milestone closeout

The complete repository gate passed with 138 tests and 77 subtests, zero Pyright diagnostics,
warning-strict execution, package builds, contract checks, and both benchmark smoke gates. The
clean 1,000-node benchmark passed all maintained thresholds and is interpreted in
`docs/MILESTONE_1_BASELINE.md`. Compatibility, measured decisions, limitations, and scope evidence
are frozen in `docs/MILESTONE_1_CLOSEOUT.md`.

Milestone 1 made no storage rewrite, self-hosting change, production integration change, tag, or
release.

### Initial design constraints

- Full rebuild remains the recovery and equivalence oracle.
- Canonical content remains authoritative.
- Existing one-method `load_projection()` adapters remain unchanged.
- No-AST adapters remain first-class.
- Indexes, source-generation receipts, and caches remain disposable.
- Cheap reads may trust only identity-bound, versioned, corruption-checked receipts.
- Any optimization must fail closed on source mutation and must preserve stale-read refusal.

### Future ideas and suggestions

These are notes, not commitments:

- A stable source-generation provider may deserve a public adapter capability only after both the
  generic project and one incremental adapter prove the same boundary.
- Profiling receipts could eventually feed the human-facing project control panel, but Milestone 1
  should expose structured data before adding UI.
- A durable telemetry exporter remains deliberately deferred. Request-local bounded aggregates are
  enough to prove compiler work in Milestone 1 without adding persistence, cardinality, or privacy
  risks.
- The stat identity is a cheap publication proof, not a cryptographic integrity scan. Full index
  validation remains the launch and query oracle.
- Cursor authentication remains deliberately absent. If read cursors ever carry authority rather
  than bounded positions, they will need a different versioned security contract and persisted key
  lifecycle.

## Milestone 2 — complete: agent retrieval and MCP experience

### Audit reconciliation

Three independent read-only audits covered effective policy and bootstrap, task-shaped retrieval
and context capsules, and generation diffs plus client configuration and doctor checks.

They agreed on these boundaries:

- Keep the project descriptor at schema version 1. Process capability and client configuration are
  machine-specific bindings, not canonical project content.
- Preserve the legacy adapter-policy payload, no-AST shorthand, tool names, default tool ordering,
  one-method adapters, and custom context provider.
- Add one versioned effective-policy authority and derive bootstrap, contract, instructions, and
  access reporting from it.
- Add one task-context operation with a closed task-kind vocabulary and one immutable,
  generation-pinned retrieval plan. Do not create a tool for every task kind.
- Produce evidence gaps only from declared plan requirements and completed bounded checks. Never
  infer missing facts from arbitrary project naming.
- Record only the latest bounded generation transition as disposable evidence. Do not add a
  history database.
- Preview client configuration by default. Any write must be explicit, atomic, merge-preserving,
  and backed by a verified client-format driver.
- Keep doctor strictly read-only. It must not bootstrap, synchronize, build, render, start a
  viewer, or rewrite client configuration.

### Versioned effective policy and session contract

The binding now composes an immutable version-1 policy containing capability mode, adapter
evolution, AST and Logic behavior, synchronization and integrity levels, render and viewer
behavior, profiling, blocked tools, prohibitions, and explicit precedence. `--no-ast` is a
restrictive override. The exact legacy `adapter_policy` response remains a projection of the new
object.

Bootstrap reuses the identity already proven by synchronization and no longer reloads the complete
project. Its additive version-1 session contract reports binding, generation, effective policy,
actual registered surfaces and mutation access, render policies, first operation, filtered
workflow, and prohibitions. Read mode does not recommend proposals. Proposal mode recommends
registration and review only with writer access. Application is recommended only when the
exact-hash applier is enabled.

Existing factory defaults and tool order remain unchanged. Explicit application mode fails closed
without an applier. Operator mode is reserved and currently adds no tools.

### Versioned task retrieval and context capsules

The first Milestone 2 retrieval slice adds one `docforge_get_task_context` read tool rather than a
family of task-specific tools. Its closed task kinds are change, implementation, failure,
ownership, test, operation, and release. One immutable `RetrievalPlanV1` derives exact or lexical
focus, bounded bidirectional graph traversal, metadata hydration, required evidence categories,
and fixed work budgets from the project descriptor and effective policy.

The public executor re-derives every submitted plan before opening SQLite. It rejects modified
steps, task identity, requirements, category order, bounds, policy identity, or hashes as
`invalid_retrieval_plan`. Traversal binds the project relation set by canonical hash and queries
the already-validated edge table by endpoint, avoiding relation-sized SQL parameter lists.
Version-1 internal ceilings are 1,000 evidence items, 100,000 candidate edges, and 10,000 task
query characters.

The executor uses one immutable SQLite read generation. It rejects missing explicit focus, blocks
unresolved or tied lexical focus, stops at deterministic evidence and candidate-edge limits, and
checks source identity again when the transaction closes. `ContextCapsuleV1` binds the generation,
policy, request, plan, evidence collection, and complete capsule with canonical hashes.

Project relation names remain authoritative. The core recognizes only a versioned alias map for
structure, implementation, dependency, execution, data, evidence, and context. Unknown allowed
relations stay visible under their raw names as `unclassified`. Required evidence diagnostics
distinguish categories the project never declared, completed bounded checks with no selected
evidence, and incomplete checks caused by a result, work, token, or response limit.

Each evidence item carries a stable content hash, confined source identity, shortest selected graph
path, every additional qualifying relationship reason observed during traversal, and explicit
limitations where the current graph cannot prove evidence type, extractor identity, relationship
source provenance, or observation time. The planner contains no Logic operation, so no-AST
bindings can use task context without weakening their existing Logic prohibition.

Path direction is relative to the preceding traversal node. Additional relationship reasons use
the evidence node as their direction subject. Candidate-edge and unclassified-relation ceilings
produce explicit omissions and bounded summaries.

MCP pagination preserves the complete plan, collection, and capsule hashes while returning bounded
pages. Its cursor additionally binds the effective policy and task request. An individually
oversized item advances once as a hash-identified omission. A later generation or policy change
fails closed as `stale_cursor`.

The legacy profile-context contract remains intact. A custom context provider does not silently
gain core task planning. Version 1 defines no custom task-planner extension, so the additive tool
returns `task_context_unavailable` without synchronization or a complete projection load.

Two independent pre-commit audits reproduced and closed plan-forgery, relation-sized SQL,
SQLite-parameter portability, ambiguous relationship-direction, missing work-limit evidence,
schema/runtime drift, incomplete page hashing, and custom-provider hidden-load defects. Regression
coverage includes 33,005 valid relation names, fixed extreme project limits, tampered plans,
evidence-relative directions, edge and unclassified limits, schema-valid pages, changed cursor
semantics, oversized evidence advancement, no-AST retrieval, and legacy complete-projection
adapters.

The complete repository gate passes with 158 tests and 101 subtests, zero Pyright diagnostics,
warning-strict execution, package builds, public-contract validation, and the maintained Milestone
0 and Milestone 1 smoke benchmarks. Gitleaks 8.30.1 reports no secret findings in the working tree.

### Latest-generation diff receipt

Three read-only audits reconciled the index publication, public transport, compatibility, and
no-AST boundaries before implementation. The selected design stores one disposable
`generation-diff.json` receipt. It does not add a history database, arbitrary generation
selectors, source text, rendered content, or Logic details.

Before a build loads current source, it accepts an existing index only when its exact main-file
inode has a matching stable whole-file attestation and no WAL, journal, or shared-memory sidecar.
It then captures that predecessor through an immutable main-file transaction. The capture validates
the SQLite application and schema IDs, project/root/adapter binding, integrity, complete node and
edge rows, Logic aggregate identity, FTS count, metadata hashes and counts, and final file
signature. It never calls normal check or synchronization and never repairs predecessor evidence.

The final source revalidation now compares exact nodes and edges in addition to source hash,
revision, and Logic. A verified predecessor that maps the same source identity to different graph
content fails before publication as `generation_collision`. This closes a pre-existing adapter
determinism gap found during the generation-diff audit.

SQLite replacement is now the explicit derived mutation commit point. Whole-file attestation,
cheap source-generation, and generation-diff receipts publish independently afterward. Any
post-commit receipt failure returns `status = ok`, `index = published`, a bounded degraded
publication record, and receipt-stage names. It never rolls back the new index or reports a false failed
mutation. Attestation hashing checks the exact index signature before, during, and immediately
before receipt publication.

Version-1 diff semantics compare every core `Node` field by stable node ID and exact edge triples.
Node renames are removal plus addition. Edge changes are removal plus addition. Exact summary
counts and a full ordered item-hash collection cover every change. Retained details are
deterministically ordered and independently capped at 1,000 items and 1 MiB with explicit item- or
byte-limit evidence. A first build or untrusted predecessor is a baseline with no fabricated
all-added result. A same-generation reindex republishes the existing meaningful transition against
the new index file identity instead of erasing it with an empty diff.

The additive public surfaces are:

- CLI `generation-diff [--limit N] [--cursor OPAQUE]`.
- MCP `docforge_get_generation_diff(limit=None, cursor=None)`.
- Telemetry operations `cli.generation-diff` and `mcp.generation_diff`.

Public reads do not open SQLite, call `project.load()`, extract an adapter projection, parse source,
check, synchronize, build, or repair. They strictly validate the bounded receipt, compare stable
receipt and index file identities, require two matching cheap source-generation checks, and report
unknown for legacy adapters without that capability. Missing, corrupt, foreign, oversized,
symlinked, stale, or concurrently changed evidence remains a read-only status outcome.

Generation-diff pagination binds the complete stored receipt hash and effective policy. That hash
already covers project, generation, graph, collection, and committed-index identity. Page size may
change. A replaced receipt returns `stale_cursor`. One top-level pagination object owns the only
cursor. The nested version-1 page uses `receipt_header.stored_receipt_hash` so it never
misrepresents the complete receipt hash as the hash of a partial header. The summary distinguishes
additional retained pages from details permanently omitted by the fixed publication limits.

Adversarial coverage now includes strict runtime/schema rejection, predecessor attestation and
generation identity, live and synthetic SQLite sidecars, cache-root symlink substitution,
source/sidecar changes during diff preparation, independent receipt failures, and degraded
post-commit identity and durability failures. Focused verification passes the direct, CLI, MCP,
schema, pagination, legacy, incremental no-AST, and zero-work suites. The complete repository gate
passes with 176 tests and 113 subtests, zero Pyright diagnostics, package builds, web checks, and
the maintained Milestone 0 and Milestone 1 smoke benchmarks. Final independent re-audit is in
progress before this slice is committed.

The final dense benchmark uses a 1,000-node transition with 1,000 changed details. Its receipt is
775,663 bytes. Direct status is 37.659 ms median and 39.108 ms p95. A maximum-size MCP request
returns 307 items in 199,754 bytes at 54.037 ms median and 56.617 ms p95. Four pages reconstruct
all 1,000 retained details in 652,798 bytes at 201.55 ms median. Peak RSS is 79,096 KiB.
Every hidden-work counter remains zero; the read performs exactly two cheap source-generation
checks.

Measurement found and removed two avoidable costs before commit. Receipt loading had repeated the
complete 1,000-item validator solely to check project identity; it now validates once and compares
the three binding fields directly. Page fitting had encoded every growing prefix; it now uses an
exact logarithmic search and retains the hash-only oversized-item omission path. The maximum page
fell from 272.06 ms p95 to 56.617 ms p95, while full traversal fell from roughly 859 ms to
203.55 ms p95. Regression tests require one receipt validation and at most 15 response encodes for
1,000 page candidates. Final independent publication, contract, and performance audits approve
the slice for commit.

### Deterministic client configuration and read-only doctor

Client integration remains an explicit machine-local boundary rather than canonical project
content. `docforge configure {codex,claude,openclaw} --project PATH` previews a deterministic
version-1 fragment by default. An optional output path publishes only a standalone fragment into
an existing real directory. Publication is create-only, private-mode, no-follow, bounded, and
conflict-aware. Existing differing client configuration is never merged, replaced, or silently
overwritten.

Generated commands use the exact current virtual-environment Python executable with isolated
module startup. The binding records explicit read, proposal, or application mode, no-AST policy,
render policy, empty environment, and bounded timeouts. Proposal and application generation fail
closed unless the descriptor declares the required writer and matching applier identity. A generic
CLI cannot reconstruct project-owned adapter composition, so custom adapters return an explicit
unavailable result instead of generating a misleading command.

Codex and OpenClaw fragments include their verified timeout fields. Claude JSON fragment syntax is
supported, while its timeout representation remains an explicit warning. The configuration result
has a strict JSON schema and canonical plan hash. Diagnostics are additive and remain disabled by
default.

`docforge doctor --client CLIENT` performs bounded, non-mutating inspection only. It reads the
project descriptor and selected client file through stable, directory-bound, no-follow handles;
parses at most 1 MiB and 256 server entries; selects at most one exact project binding; validates
the closed server argument set; checks executable, capability, declared authority, no-AST,
timeouts, environment-key names, and tool-filter presence; and performs only a stat-level index
presence check. It never loads canonical sources, opens SQLite, starts MCP, executes the configured
command, synchronizes, builds, renders, starts a viewer, or writes client configuration.

Doctor reports healthy, degraded, or unhealthy with stable process exit codes 0, 1, and 2. Secret
environment values are parsed only to enforce bounded string limits and are never returned.
Unknown or unverified client tool filtering, Claude timeout representation, implicit legacy
capability mode, shadowed authority, and missing disposable indexes are warnings. Unsafe paths,
malformed matching entries, unexpected executables, wrong project roots, invalid authorities, and
missing configuration are failures.

The first benchmark smoke failed for the correct product reason: its disposable doctor fragment
used the shared path `/tmp/doctor-codex.toml`, where a previous run had left different content. The
harness now creates a project subdirectory inside one unique temporary root and places the client
fragment beside it. This preserves create-only conflict safety and makes every run disposable.

The final pre-commit 1,000-node audit sample passes every provisional Milestone 2 gate. Task
context reconstructs 1,000 candidates as 108 cited evidence records and 892 explicit bounded
omissions across 11 pages in 703.808 ms. Generation diff reconstructs 1,000 changed details across
10 pages in 427.450 ms. Maximum pages remain below the 200,000-byte MCP budget; generation diff
uses 199,566 bytes and proves that diagnostics are discarded before the primary result. Isolated
peak RSS is 86,168 KiB.

Configuration preview now includes a bounded real import probe of the exact isolated interpreter,
so its provisional single-sample latency is about 315 ms rather than the earlier sub-millisecond
derivation-only figure. Doctor remains below 1 ms on generated disposable configurations.
Every configuration and doctor hidden-work counter is zero.

The aggregate `make gate` includes the Milestone 2 smoke benchmark. The frozen candidate passes
205 tests and 120 schema subtests, strict warnings, Ruff, formatting, Pyright, web checks,
compilation, lock and dependency checks, package builds, and all three milestone smoke benchmarks.
Three independent final audits approve client publication and policy binding, doctor fail-closed
behavior, and benchmark/contract coverage. Clean-revision benchmark evidence is still required
before closeout.

### Milestone 2 closeout

Candidate commit `fb0df5e4a1c591c2a84788fd4814d98550f11863` passed the clean ten-sample
Milestone 2 benchmark. Task-context complete traversal measured 703.561 ms median and 721.847 ms
p95 across 11 bounded pages. It reconstructed the exact 1,000-candidate collection from 108 cited
evidence records, 891 original token-budget omissions, and one hash-attested response-limit
surrogate. Generation-diff complete traversal measured 418.607 ms median and 425.315 ms p95 across
10 pages.

Read and no-AST bootstrap remained below 10 ms p95. The maximum generation page used 199,566 bytes
of the 200,000-byte budget and correctly discarded diagnostics before primary evidence.
Configuration preview measured about 314 ms median and 365 ms p95 because it proves the real
isolated interpreter import on every invocation. Codex and OpenClaw doctor checks remained below
0.6 ms p95; Claude remained explicitly degraded because its timeout format is unverified.
Isolated-process peak RSS was 86,448 KiB against the 262,144 KiB gate.

All measured configuration and doctor counters were zero. Task-context pages performed one index
check and two cheap generation checks with no loads, parses, synchronization, builds, extraction,
rendering, or viewer work. Generation-diff pages performed two cheap generation checks and no
index check. The canonical machine-readable result is
`benchmarks/milestone2-2026-07-29.json`.

Milestone 2 is complete. Follow-up ideas stay explicitly later-scope: avoid recomputing the
task-shaped capsule for every continuation page, add authenticated continuation when the threat
model requires it, verify a native Claude timeout representation, and introduce adapter-owned
launcher metadata before generating configurations for custom adapters.

## Milestone 3 — complete: independent projections

Milestone 3 began only after `main` and `dev` were aligned at the verified Milestone 2 closeout.
Three read-only audits ran before source changes:

- Manual planning, immutable packages, renderer isolation, receipts, preview/application
  integration, and full/incremental equivalence.
- Portable graph planning, static artifacts, the live viewer boundary, worker protocol, and static
  plus interactive accessibility.
- Packaging, optional dependencies, public contracts, projection policies, performance,
  incremental fragments, and maintained gates.

The active design constraints are unchanged: renderers consume one validated immutable generation;
manual and graph plans remain separate; the live viewer is not retrieval authority; core remains
usable without rendering; status performs no hidden rendering; full rendering remains the recovery
and equivalence oracle; no storage rewrite is assumed.

### Milestone 3 architecture decision

The three audits converged on one compatibility-first boundary:

- The existing `docforge.render_contract` names, `GenericHtmlRenderer.prepare()` signature,
  `generic_html` renderer identity, and byte output remain the version-1 compatibility surface.
  They become adapters over the new manual-planning path rather than being changed in place.
- New `ManualRenderPlanV1`, `GraphViewPlanV1`, `ProjectionPackageV1`, and
  `ProjectionReceiptV1` contracts use strict canonical JSON, deterministic ordering, independent
  item and byte bounds, exact generation and policy binding, and content-derived identities.
- Plans and packages contain selected graph facts and bounded content. They never contain a
  project object, SQLite handle, absolute project or index path, arbitrary query, command, or
  project-provided executable code.
- The planner owns graph selection and meaning. A renderer may transform only a validated package
  into declared artifacts and cannot select nodes, invent relationships, crawl the project, choose
  publication paths, or mutate canonical sources.
- Manual and portable graph renderers live behind independent import boundaries. Renderer
  dependencies load lazily. Default installation behavior remains compatible during the initial
  migration; optional dependency changes require their own verified packaging decision.
- Portable graph rendering is additive. It does not replace or silently change
  `docforge_visualize`, `graph-browser@17`, the viewer-manager protocol, or the query-backed live
  viewer.
- Effective policy version 1 remains frozen. Milestone 3 introduces a version-2 projection-policy
  view for manual `auto|explicit|disabled`, portable graph `explicit|disabled`, and live viewer
  `on-demand|disabled` enforcement, while retaining the version-1 projection for existing clients.
- Publication commits content-addressed artifacts first, renderer evidence second, and a bounded
  generation/view manifest last. Status remains receipt-only. Failures after artifact replacement
  report committed degraded success rather than an ordinary failed mutation.
- Full planning and rendering remain the recovery and equivalence oracle. Incremental fragments
  are disposable, keyed from complete plan semantics, and may be reused only when byte-exact
  artifact equivalence is proven.
- The live source endpoint must stop reading mutable canonical files behind a pinned graph
  snapshot. Portable artifacts never inherit that path-bearing behavior.

The first implementation slice freezes existing golden output, adds the four versioned contracts
and validators, introduces pure manual and graph planners, and makes the legacy manual renderer a
compatibility wrapper. Publication hardening, detached rendering, incremental fragments, portable
graph publication, independent policy enforcement, accessibility, and maintained performance
gates follow on top of that frozen boundary.

### Milestone 3 contract slice

The first slice now implements:

- Strict Draft 2020-12 schemas and runtime canonical-hash validation for manual plans, graph plans,
  projection packages, and projection receipts.
- A deterministic manual planner that owns page selection, navigation, cross-references,
  backlinks, search documents, component assignments, orphan diagnostics, and cycle diagnostics.
- A deterministic graph planner with exact-root or metadata-only lexical scope, closed filters,
  explicit node/edge/work bounds, deterministic omissions, path/source-body exclusion, and
  no-AST Logic exclusion.
- A separate `docforge_renderers.manual` package. Its renderer accepts only a validated package and
  has no project, SQLite, publication-path, or filesystem-write API.
- The frozen `GenericHtmlRenderer` compatibility shim over the new planner/package/renderer
  pipeline. The alpha artifact remains exactly 2,043 bytes with output SHA-256
  `81656bb89debc7ad1fbe8bc290e9a3ba90664442b17a6d57e908d30d20c47f77` and legacy render identity
  `1c0a49c28ba3b0dabf94be36e75def197dee1be3cb73ac405b09875383c8dc5f`.
- Rejection of project-template scripts, inline event handlers, `javascript:` URLs, embedded
  browsing contexts, and refresh redirects.
- Wheel inclusion for both typed packages and every published JSON schema. Importing `docforge`
  no longer imports `markdown_it` or the manual renderer package.
- A live-viewer correction: source evidence now comes from the pinned index generation. The
  viewer no longer reopens mutable canonical files behind an older graph snapshot.

The new repository-native contract target passed 91 tests and 120 subtests at the slice boundary.
The combined projection, rendering, and live-viewer focus passed with byte-exact compatibility and
no hidden source/path authority.

### Durable portable graph publication

The portable graph path now has its own declared `graph_render` views, pure plans, fixed
`portable_graph_html` renderer, content-addressed artifact store, renderer receipts, and one bounded
generation/view manifest as the publication commit. It supports Nodes, Flow, and Web without
including Logic. Static HTML contains the complete pre-rendered graph and treats JavaScript as
progressive enhancement.

Publication revalidates source, view, artifact, receipt, and output identities across replacement.
Status reads only bounded manifest and receipt evidence. It never plans or renders. Repair may
restore a declared output from its content-addressed artifact. A post-artifact failure that cannot
be rolled back returns explicit degraded committed evidence rather than reporting an ordinary
failed mutation.

### Detached workers and incremental fragments

Manual and portable graph packages execute through one fixed one-request child protocol. The
parent launches isolated Python from a trusted working directory with a sanitized environment,
spools stdout to disk, reads one bounded canonical response, and validates the complete artifact
and receipt identity. The worker accepts only the two built-in renderer identities. Requests are
bounded by the 24,000,000-byte package contract, actual artifact transfer by 20,000,000 bytes, and
execution by a 30-second timeout.

Manual fragment records are semantic, versioned, canonical, hash-bound, and stored below a
dedicated confined cache. The worker independently recomputes the expected page fragment before
using a record. Corrupt, forged, oversized, stale, or aggregate-oversized records fall back to the
full detached render. Cold fragment creation is compared byte-for-byte with that full oracle before
cache publication. The cache retains only the current inventory and is capped at 10,000 entries
and 64,000,000 bytes.

### Independent policies and accessibility

Projection policy version 2 independently composes manual `auto|explicit|disabled`, portable graph
`explicit|disabled`, and live viewer `on-demand|disabled`. CLI, MCP, generated client
configuration, doctor, render services, canonical application, onboarding, and viewer-manager
entry points enforce their relevant policy. Status remains available when an active operation is
disabled.

Generated client evidence binds the projection policy, its hash, projection availability, and the
current descriptor hash into the configuration hash. Validation cross-checks omitted default
selectors against the bound descriptor so coordinated policy and availability drift fails closed.
The version-1 effective-policy payload remains unchanged for existing clients.

Pinned Playwright 1.62.0 and axe-core 4.12.1 gates exercise the frozen manual, portable graph, and
live viewer with selected WCAG A/AA axe tags and keyboard interaction flows. Portable and live
graph presentation received only the minimal contrast and nested-role corrections needed by those
gates.

### Scale and runtime hardening

The first 1,000-node full benchmark exposed recursive strongly connected-component traversal in
manual planning. Cycle detection now uses an iterative two-pass traversal. A regression covers the
descriptor maximum of 10,000 nodes as both a deep acyclic chain and one strongly connected
component.

The isolated wheel proof also exposed a Python `runpy` warning when the worker module was imported
during package initialization before `-m` execution. A private fixed module entrypoint now owns
child startup. Malformed child input returns code 2 with empty stdout and stderr.

Configured render ceilings above 20,000,000 bytes remain accepted for compatibility, and small
actual artifacts render normally. The detached protocol still rejects an actual transfer beyond
its fixed 20,000,000-byte boundary.

### Milestone 3 closeout

Candidate `f5dccb5e1c312121f1af63780162f593d9363b98` passed the complete repository gate: formatting,
Python and web lint, strict types, compilation, 281 tests and 272 subtests, three accessibility
flows, lock and dependency checks, package builds, and all milestone smoke benchmarks. The
maintained projection contract subset passed 142 tests and 236 subtests.

The clean ten-sample 1,000-node benchmark passed every latency, memory, response-size, no-work, and
equivalence gate. Manual full rendering measured 810.490 ms p95, portable graph full rendering
323.690 ms p95, and receipt-only status 111.381 ms and 59.331 ms p95 respectively. Direct detached
worker peaks were 88,580,096 and 89,583,616 bytes. The separately gated production manual worker
peak was 104,771,584 bytes. Production cold, warm, forced-full, add, change, delete, and reorder
outputs were byte-identical.

Production warm fragment rendering measured 2,206.540 ms p95 versus 978.870 ms for forced full.
Milestone 3 therefore closes the fragment isolation, invalidation, equivalence, and recovery
contract without claiming a throughput win. Later optimization must begin from that evidence.

The exact method and measurements are recorded in `docs/MILESTONE_3_BASELINE.md` and
`benchmarks/milestone3-2026-07-29.json`. The candidate passed an isolated wheel CLI/MCP/worker
proof. Gitleaks 8.30.1 found no findings across the six Milestone 3 commits or candidate tree.

Milestone 3 is complete. No tag, release, production integration repointing, WorldForge change,
ScrapeStation change, storage rewrite, or self-hosting dependency was introduced. Milestone 4
remains directional and has not started.