Remove plugins/, workspace-configs-templates/, org-templates/ dirs (now
in standalone repos). Add manifest.json listing all 33 repos and
scripts/clone-manifest.sh to clone them. Both Dockerfiles now use the
manifest script instead of 33 hardcoded git-clone lines.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Part 4 of 4 — terminal step of the org.yaml scalability refactor. Each
role in the molecule-dev template now owns its own workspace.yaml file,
colocated with the existing system-prompt.md / initial-prompt.md /
idle-prompt.md / schedules/*.md. Team files shrink to a leader's own
definition plus a list of !include refs.
## Platform change
`resolveYAMLIncludes` now uses a TWO-ROOT model:
- Path resolution is relative to the INCLUDING file's directory
(natural sibling + cousin refs, C-include / Sass @import convention).
- Security bound is the ORIGINAL org root (`rootDir`), preserved across
all recursion depths. Sibling-dir refs like `../my-role/workspace.yaml`
from a team file are now allowed (they stay inside the org template);
refs that escape the root still error.
Regression coverage: new `TestResolveYAMLIncludes_SiblingDirAccess`
reproduces the Phase 4 pattern (team file at `teams/x.yaml` referencing
`../<role>/workspace.yaml`) — fails without the fix, passes with.
## Template change
Atomized 15 child workspaces across 3 team files:
- `teams/research.yaml`: 58 → 30 lines; 3 children now !include refs
- `teams/dev.yaml`: 222 → 38 lines; 6 children now !include refs
- `teams/marketing.yaml`: 143 → 28 lines; 6 children now !include refs
Each role now has `<role>/workspace.yaml` colocated with its prompts.
Example `frontend-engineer/` directory:
frontend-engineer/
├── workspace.yaml (24 lines — name/role/tier/canvas/plugins/...)
├── system-prompt.md (from earlier phases)
├── initial-prompt.md
├── idle-prompt.md
└── (no schedules for this role — but if added, schedules/<slug>.md)
## File-size progression across all 4 phases
| State | org.yaml | total `.yaml` in tree |
|---|---:|---:|
| Before (main) | 1801 lines / 108 KB | 1801 / 108 KB (one file) |
| After Phase 1 (#389) | 1687 | 1687 / 101 KB |
| After Phase 2 (#390) | 676 | 676 / 35 KB |
| After Phase 3 (#393) | 114 | 683 (1 + 6 teams) / 33 KB |
| **After this PR** | **114** | **~698** (1 + 6 + 15 workspace) / 35 KB |
Aggregate size is flat — the decrease came from prompt externalization
in Phases 1/2; Phases 3/4 reorganize structure without adding content.
The win is readability and ownership:
- Every individual file fits on 1-2 screens.
- Adding a new role is now: create `<role>/` dir, add `workspace.yaml`
+ `system-prompt.md` + prompts, add ONE `!include` line to the team
file. No touching of aggregated mega-YAML.
- Team files can be reviewed + merged independently.
## Tests
All 10 `TestResolveYAMLIncludes_*` tests pass, including the real-template
integration test (`TestResolveYAMLIncludes_RealMoleculeDev`) which now
walks org.yaml → teams/pm.yaml → teams/research.yaml → ../market-analyst/
workspace.yaml and validates the full 21-role tree unmarshals cleanly.
Plus all existing `TestResolvePromptRef` + `TestOrgYAML` + `TestInitialPrompt`
suites stay green.
## Ops followup
After merging all 4 phases and deploying, the `POST /org/import`
endpoint should produce a workspace tree byte-identical to the
pre-refactor state. Verify with:
diff <(curl POST /org/import before) <(curl POST /org/import after)
or by spot-checking:
- `/configs/config.yaml` bodies across all 21 workspaces
- `workspace_schedules.prompt` row values
The externalization is lossless — YAML literal to file and back
recovers the same string modulo trailing-whitespace normalization.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Part 2 of 4 in the org.yaml scalability refactor. Follows PR #389 which
added platform support; this PR completes the migration for every role
in the `molecule-dev` template.
## Scope
All 20 remaining roles moved from inline YAML literals to sibling .md
files under their existing `files_dir`:
- PM, Research Lead, Dev Lead, Marketing Lead (4 leaders)
- Market Analyst, Technical Researcher, Competitive Intelligence (research)
- Frontend/Backend/DevOps Engineer, Security Auditor, QA Engineer, UIUX
Designer, Triage Operator (dev team)
- DevRel, PMM, Content Marketer, Community Manager, SEO Growth Analyst,
Social Media Brand (marketing team)
Per workspace, externalized (where present):
- `initial_prompt: |...` → `initial-prompt.md` + `initial_prompt_file:`
- `idle_prompt: |...` → `idle-prompt.md` + `idle_prompt_file:`
- `schedules[*].prompt: |...` → `schedules/<slug>.md` + `prompt_file:`
Totals: 17 initial-prompt files, 12 idle-prompt files, 18 schedule files
(47 new files).
## File-size impact
| Before (main) | After Phase 1 | After Phase 2 | Reduction |
|---|---|---|---|
| 1801 lines | 1687 lines | 676 lines | **-62.5%** |
| 108 KB | 101 KB | 35 KB | **-67%** |
org.yaml is now pure structural scaffolding (name / role / tier / model /
canvas / plugins / channels / children / category_routing / schedules
metadata). Readable end-to-end on one screen per team.
## How the migration was driven
A Python round-trip script (using `ruamel.yaml` to preserve comments +
formatting) walked the workspace tree recursively, wrote prompts to
files keyed by `files_dir`, and replaced inline keys with `*_file:` refs.
Zero manual YAML hand-editing beyond the Phase 1 Documentation Specialist
proof. Script is one-shot; not committed.
Slug convention for schedule files: lowercase the schedule name, replace
non-alphanumeric with `-`, collapse, cap 60 chars. Examples:
- "Orchestrator pulse" → `orchestrator-pulse.md`
- "Hourly template fitness audit" → `hourly-template-fitness-audit.md`
- "Code quality audit (every 12h)" → `code-quality-audit-every-12h.md`
## Backwards compatibility
Fully compatible — Phase 1's resolver prefers inline when both are set,
so a future one-off experiment can still drop inline YAML. The migration
doesn't remove inline support, just stops using it.
## Verification
- [x] `python -c "yaml.safe_load(...)"` on edited org.yaml — parses clean
- [x] Walk-and-inspect script: every workspace has exactly the expected
`*_file:` refs, zero `INLINE_*` markers remain
- [x] All 47 extracted .md files non-empty + trimmed
- [x] `go test -run 'TestResolvePromptRef|TestOrgYAML|TestInitialPrompt'`
passes (from Phase 1 platform work)
- [ ] Post-merge: live `POST /org/import` against a fresh workspace,
diff the resulting `/configs/config.yaml` + `workspace_schedules`
rows against the pre-migration values (should be identical bodies)
## What's next
- **Phase 3 (queued):** YAML `!include` directive for org.yaml; split the
remaining 676 lines into `teams/{research,dev,marketing,ops}.yaml`.
- **Phase 4 (queued):** per-workspace atomization; each role owns its
own `workspace.yaml` manifest.
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Two recent platform-level security changes (#319 channel_config
encryption, #337 constant-time webhook_secret compare) were not
reflected in the Security Auditor's system prompt or the schedule cron
prompt. That meant the auditor wouldn't proactively look for the
*next* instance of either class — a new credential field added to
channel_config without being added to sensitiveFields, or a new
secret comparison using raw `!=`, would slip through until a human
happened to notice.
Updated two files:
1. org-templates/molecule-dev/security-auditor/system-prompt.md
Added two bullets to "What You Check":
- Secret comparisons must use subtle.ConstantTimeCompare /
crypto.timingSafeEqual (cites #337 as the repo's recent instance)
- Secret storage at rest: any new channel_config credential field
must be added to sensitiveFields and exercised in both the
Encrypt (write) and Decrypt (read) boundary helpers, and the
ec1: prefix must never leak into API responses (cites #319)
2. org-templates/molecule-dev/org.yaml
Same two checks added to the Security Auditor's 12-hour cron
prompt's "MANUAL REVIEW of every changed file" section. Wording
is concrete enough to paste into a grep: "flag any `!=` / `==` /
bytes.Equal against a user-supplied value that gates auth".
Pure config / prompt — no code changes, no tests to write. YAML parse
verified, TestPlugins_UnionWithDefaults still passes.
Closes#342
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Closes#248. Three instances of the same YAML-injection bug class
(#221 name/role, #233 template path, #241 runtime/model) shipped in
this repo over the last weeks. The common root cause is the Security
Auditor's system prompt didn't list YAML injection as an explicit
check class, so audits missed the pattern every time.
Adds:
- "YAML injection" to the 'Think like an attacker' list in How You Work
- An explicit entry in What You Check with the three prior instances
cited so future auditors see the pattern and the fix shape
(double-quoted scalars or a proper YAML encoder)
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
