Battam1111/Myco

v0.5.16 — 2026-04-22 — Global substrate registry + auto-germ advice + graft --list-substrates

Contract-layer molt with zero contract-surface deltas. Third
ergonomic release in the one-劳永逸 arc (v0.5.14 + v0.5.15 + v0.5.16).
Closes the last three cross-project UX gaps: operators need to be
able to enumerate every substrate they've germinated, germinate
a new one inside a workspace the host has opened without seeing an
error, and have the registry accumulate on its own without manual
intervention.

What changed

• Nothing in the R1–R7 rule text.
• Nothing in the category enum / exit-policy / exit codes.
• Nothing in the 18-verb manifest surface. (Graft grew a flag,
  not a new verb.)
• Nothing in the dimension roster count (still 25).

Added — ~/.myco/substrates.yaml global substrate registry

New module myco.core.registry:

• register_substrate(id, path) — upsert a row. Idempotent.
• touch_substrate(id, path) — best-effort last-seen update.
• list_substrates() — enumerate all, sorted by recency.
• SubstrateEntry.exists — live vs stale filter.

File format: YAML map keyed by substrate_id, one row per
substrate with path / registered_at / last_seen_at.
Atomically written via atomic_utf8_write; concurrent writes
never corrupt. Malformed files degrade to empty registry — never
raises into the calling code.

Per-user only; never shared across machines; never committed to
VCS. Mirrors shell-history / editor-recent-files semantics.

Added — germinate → registry auto-hook

myco.germination.germinate.bootstrap now calls
register_substrate() on every successful (non---dry-run)
germination. Failures (disk full, perms) are swallowed — a
registry-write error must never break germination. --dry-run
skips the registry write entirely, matching its "write nothing"
contract.

Added — myco graft --list-substrates flag

New mode on the existing graft verb. Mutually-exclusive with
--list / --validate / --explain. Returns the full
registry (across projects) with count / live_count /
stale_count counters. Example payload entry:

{
  "substrate_id": "c3-neurips2026",
  "path": "C:\\Users\\10350\\Desktop\\C3",
  "registered_at": "2026-04-22T13:29:11+00:00",
  "last_seen_at":  "2026-04-23T09:14:05+00:00",
  "exists": true
}

Agent tooling integrates via the myco_graft MCP tool's new
list_substrates kwarg.

Added — auto-germ advice soft response in _invoke

When the MCP client exposes a workspace root (via roots/list)
but that root has no _canon.yaml, v0.5.15 would raise
SubstrateNotFound with a message. v0.5.16 upgrades the UX:
the MCP layer catches the exception, captures the first file://
root from the client via a new _detect_workspace_root helper,
and returns a SOFT response whose substrate_pulse.rules_hint
tells the agent to call myco_germinate with the workspace path.

exit_code stays 4 (the canonical SubstrateNotFound code per
v0.5.8's contract), the payload carries workspace_root as a
first-class field, and the agent reads the advice and offers to
germinate. Never auto-germinates silently — that would be surprising.

Break from v0.5.15

None at the contract layer. Operators upgrading from v0.5.15
require no code, canon, or script changes.

Observable deltas:

• myco germinate writes a row to ~/.myco/substrates.yaml
  on every successful non-dry-run call. Users who want to opt out
  can rm ~/.myco/substrates.yaml at any time; Myco reads None
  gracefully. Future doctrine work may add a canon opt-out
  flag; today the registry is always-on.
• Fresh workspaces opened in Cowork / Claude Desktop / Cursor / …
  used to surface SubstrateNotFound errors on the first Myco
  tool call. They now surface a germinate-this-workspace hint in
  the pulse sidecar instead, which the agent can relay.
• myco graft now has a fourth mode (--list-substrates)
  in addition to --list / --validate / --explain.
  Existing invocations unchanged.