Remove disable_permalinks and make note permalinks invariant

[phernandez]

Problem

BasicMemoryConfig.disable_permalinks creates a second Markdown identity regime where canonical notes can lack permalinks. That now conflicts with the accepted-change journal in #1382, and it also forces every projector, linker, resolver, and replay consumer to support a nullable canonical identity.

Exact-head review surfaced the immediate failure: #1382 (comment)

Direction

Remove the disable_permalinks feature instead of spreading nullable-permalink compatibility through the journal and Wiki stack. Canonical Markdown notes should always receive a permalink.

Concrete follow-up

• Remove the configuration flag and the conditional paths that intentionally leave Markdown entity permalinks unset.
• Keep permalink assignment as an invariant at canonical note mutation boundaries.
• Remove or rewrite tests and documentation for permalink-disabled projects.
• Define the upgrade behavior for any persisted configuration that still sets the flag, failing clearly rather than silently producing identity-less notes.
• Add regression coverage proving create, update, edit, move, delete, and accepted-change replay always carry canonical permalink identity.

Acceptance

There is one Markdown identity model: every accepted canonical note mutation has a non-null permalink, and the ordered accepted-change journal/projector contract requires no nullable fallback.

[claude]

Claude finished @phernandez's task in 52s —— View job

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Triage

Type: Bug — record_accepted_project_note_change() (introduced in core PR #1382) raises when entity.permalink is None, which is the expected state for new Markdown entities when BasicMemoryConfig.disable_permalinks=True. This turns otherwise-valid create/update/edit/move/delete note mutations into server errors and rollbacks for any project running with permalinks disabled.

Priority: High — disable_permalinks is a supported, documented config path (see config_models.py, entity_service.py), and this issue makes core note mutations fail outright whenever it's enabled, not just an edge case.

Component: Core / indexing (accepted-change journaling, runtime contract, migrations) — not Cloud-specific, so no cloud label applied. Related code lives under src/basic_memory/indexing/, src/basic_memory/runtime/, and the accepted-change persistence/migration layer introduced by #1382.

Complexity: Complex — the requested fix spans the accepted-change model, an Alembic migration, the runtime contract, and the serialization boundary, plus defining fallback projector/link behavior (canonical path or external identity) when no permalink exists, with regression coverage across create/update and delete/move under disable_permalinks=True.

Duplicate check: No existing open/closed issue matches this (searched for record_accepted_project_note_change, disable_permalinks accepted change, permalink journaling). Note that record_accepted_project_note_change() isn't present on main yet, confirming this is tracking a review finding on PR #1382 (discussion) before/as that work lands, rather than a regression already shipped.

Repro steps: Not required — the issue is grounded in a concrete code-review finding with a linked discussion thread and clear acceptance criteria.

Labels applied: bug (component: none, not cloud-specific).

[phernandez]

Product direction confirmed for the follow-up: permalink is a required Core invariant. Remove the disabled-permalink regime; do not add a nullable bridge or legacy migration path. Cloud always supplies canonical permalinks, so Cloud should retain one required identity contract.