v0.0.6 — v0.0.5.x cluster (4 quality + audit fixes)

Theme: v0.0.5.x cluster shipped together. Four BACKLOG-tracked follow-ups to v0.0.5, bundled because they're all small fixes / quality-of-life improvements that make every subsequent v0.0.6+ workflow cleaner. Three of the four runs hit the very 600s agent timeout that the fourth fix is making configurable — concrete validation that the friction is real.

Added

• --max-agent-timeout-ms <n> CLI flag + RunOptions.maxAgentTimeoutMs?: number (factory-runtime). Default 600_000 (unchanged). Mirrors the v0.0.3 --max-total-tokens pattern exactly: field-level addition, string-label CLI validation (NOT a new RuntimeErrorCode). Wide-blast-radius specs can raise the ceiling explicitly.
• factory.config.json — optional config file at the consumer project root. Specifies defaults for runtime: { maxIterations, maxTotalTokens, maxPromptTokens, noJudge }. Read by factory-runtime run from cwd. Precedence: CLI flag > config file > built-in default. factory init writes one with documented defaults.
• @wifo/factory-spec-review in scaffolded devDependencies (factory-core). factory init now produces a scaffold where factory spec review works on first invocation (previously the dispatch's findPackageRoot walk failed because the package wasn't installed).
• .factory-spec-review-cache in GITIGNORE_TEMPLATE (factory-core). The reviewer cache no longer shows up in git status after a fresh factory init + factory spec review run.

Fixed

• Harness strips surrounding backticks from test: paths and patterns (factory-harness). Recurring spec-authoring pitfall — parseTestLine was passing the literal token (with backticks) to bun test, which never matched any file. Caught twice now (parse-size v1, factory-runtime-v0-0-5). The SPEC_TEMPLATE backtick-guidance BACKLOG entry is now obsolete; spec authors can write either backtick-quoted or bare paths and the harness handles both.
• factory-implement-report.filesChanged is reliable (factory-runtime). Replaces the simple post-run git diff with a pre/post working-tree snapshot (tracked + untracked + content hash). Two failure modes resolved:
  • False negative on new-file-only runs (plain git diff doesn't report untracked files).
  • False positive on pre-run uncommitted changes (the agent gets attributed for files that were already dirty).
    Pre-dirty paths are filtered out — over-attributing the agent is worse than under-attributing.

Changed

• All six @wifo/factory-* packages bumped to 0.0.6 in lockstep (matches the v0.0.5 publish coordination pattern). init-templates scaffold deps bumped from ^0.0.5 to ^0.0.6.
• ROADMAP shift: v0.0.6 was originally themed /scope-project + real-product workflow. That theme moves to v0.0.7; v0.0.6 contains the v0.0.5.x cluster shipped here.

Public API surface

Unchanged across every package. Strictly equal to v0.0.5's surface (27 / 18 / ~16 / 19 / 10 / ~7). All v0.0.6 changes are field-level on already-exported types or internal-only helpers.

Package	Exports
@wifo/factory-core	27
@wifo/factory-context	18
@wifo/factory-harness	~16
@wifo/factory-runtime	19
@wifo/factory-spec-review	10
@wifo/factory-twin	~7

Test surface growth

• @wifo/factory-core: 74 → 77 (+3 init-ergonomics scenarios)
• @wifo/factory-harness: 56 → 60 (+4 backtick-stripping scenarios)
• @wifo/factory-runtime: 131 → 138 (+4 filesChanged + 3 agent-timeout scenarios)
• Workspace total: 446 → 462

Reconciliations worth knowing

• The cluster shipped as v0.0.6, not v0.0.5.1. Spec ids stay as factory-{harness,core,runtime}-v0-0-5-{1,2} (they refer to the v0.0.5 follow-up cluster). The published npm version is v0.0.6 because 4-segment versions like 0.0.5.1 aren't strict SemVer and would be rejected by the registry.
• Three of four runs hit the 600s agent timeout while implementing the cluster. The fourth fix (--max-agent-timeout-ms) is now in for the next run. Net effect: the v0.0.7 work will not hit this — the configurable knob exists.
• Lockstep bump even for unchanged packages. spec-review/context/twin didn't change in v0.0.6 but bumped to 0.0.6 anyway. Matches the v0.0.5 publish-coordination pattern; keeps the scaffold's ^0.0.6 deps uniformly resolvable.

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