fix(P1+P2): canonicalize project names at every trust boundary

Three findings from codex's review of the previous P1+P2 fix. The
earlier commit (f2372ef) only fixed alias resolution at the context
builder. Codex correctly pointed out that the same fragmentation
applies at every other place a project name crosses a boundary —
project_state writes/reads, interaction capture/listing/filtering,
memory create/queries, and reinforcement's downstream queries. Plus
a real bug in the interaction `since` filter where the storage
format and the documented ISO format don't compare cleanly.

The fix is one helper used at every boundary instead of duplicating
the resolution inline.

New helper: src/atocore/projects/registry.py::resolve_project_name
---------------------------------------------------------------
- Single canonicalization boundary for project names
- Returns the canonical project_id when the input matches any
  registered id or alias
- Returns the input unchanged for empty/None and for unregistered
  names (preserves backwards compat with hand-curated state that
  predates the registry)
- Documented as the contract that every read/write at the trust
  boundary should pass through

P1 — Trusted Project State endpoints
------------------------------------
src/atocore/context/project_state.py: set_state, get_state, and
invalidate_state now all canonicalize project_name through
resolve_project_name BEFORE looking up or creating the project row.

Before this fix:
- POST /project/state with project="p05" called ensure_project("p05")
  which created a separate row in the projects table
- The state row was attached to that alias project_id
- Later context builds canonicalized "p05" -> "p05-interferometer"
  via the builder fix from f2372ef and never found the state
- Result: trusted state silently fragmented across alias rows

After this fix:
- The alias is resolved to the canonical id at every entry point
- Two captures (one via "p05", one via "p05-interferometer") write
  to the same row
- get_state via either alias or the canonical id finds the same row

Fixes the highest-priority gap codex flagged because Trusted Project
State is supposed to be the most dependable layer in the AtoCore
trust hierarchy.

P2.a — Interaction capture project canonicalization
----------------------------------------------------
src/atocore/interactions/service.py: record_interaction now
canonicalizes project before storing, so interaction.project is
always the canonical id regardless of what the client passed.

Downstream effects:
- reinforce_from_interaction queries memories by interaction.project
  -> previously missed memories stored under canonical id
  -> now consistent because interaction.project IS the canonical id
- the extractor stamps candidates with interaction.project
  -> previously created candidates in alias buckets
  -> now creates candidates in the canonical bucket
- list_interactions(project=alias) was already broken, now fixed by
  canonicalizing the filter input on the read side too

Memory service applied the same fix:
- src/atocore/memory/service.py: create_memory and get_memories
  both canonicalize project through resolve_project_name
- This keeps stored memory.project consistent with the
  reinforcement query path

P2.b — Interaction `since` filter format normalization
------------------------------------------------------
src/atocore/interactions/service.py: new _normalize_since helper.

The bug:
- created_at is stored as 'YYYY-MM-DD HH:MM:SS' (no timezone, UTC by
  convention) so it sorts lexically and compares cleanly with the
  SQLite CURRENT_TIMESTAMP default
- The `since` parameter was documented as ISO 8601 but compared as
  a raw string against the storage format
- The lexically-greater 'T' separator means an ISO timestamp like
  '2026-04-07T12:00:00Z' is GREATER than the storage form
  '2026-04-07 12:00:00' for the same instant
- Result: a client passing ISO `since` got an empty result for any
  row from the same day, even though those rows existed and were
  technically "after" the cutoff in real-world time

The fix:
- _normalize_since accepts ISO 8601 with T, optional Z suffix,
  optional fractional seconds, optional +HH:MM offsets
- Uses datetime.fromisoformat for parsing (Python 3.11+)
- Converts to UTC and reformats as the storage format before the
  SQL comparison
- The bare storage format still works (backwards compat path is a
  regex match that returns the input unchanged)
- Unparseable input is returned as-is so the comparison degrades
  gracefully (rows just don't match) instead of raising and
  breaking the listing endpoint

builder.py refactor
-------------------
The previous P1 fix had inline canonicalization. Now it uses the
shared helper for consistency:
- import changed from get_registered_project to resolve_project_name
- the inline lookup is replaced with a single helper call
- the comment block now points at representation-authority.md for
  the canonicalization contract

New shared test fixture: tests/conftest.py::project_registry
------------------------------------------------------------
- Standardizes the registry-setup pattern that was duplicated
  across test_context_builder.py, test_project_state.py,
  test_interactions.py, and test_reinforcement.py
- Returns a callable that takes (project_id, [aliases]) tuples
  and writes them into a temp registry file with the env var
  pointed at it and config.settings reloaded
- Used by all 12 new regression tests in this commit

Tests (12 new, all green on first run)
--------------------------------------
test_project_state.py:
- test_set_state_canonicalizes_alias: write via alias, read via
  every alias and the canonical id, verify same row id
- test_get_state_canonicalizes_alias_after_canonical_write
- test_invalidate_state_canonicalizes_alias
- test_unregistered_project_state_still_works (backwards compat)

test_interactions.py:
- test_record_interaction_canonicalizes_project
- test_list_interactions_canonicalizes_project_filter
- test_list_interactions_since_accepts_iso_with_t_separator
- test_list_interactions_since_accepts_z_suffix
- test_list_interactions_since_accepts_offset
- test_list_interactions_since_storage_format_still_works

test_reinforcement.py:
- test_reinforcement_works_when_capture_uses_alias (end-to-end:
  capture under alias, seed memory under canonical, verify
  reinforcement matches)
- test_get_memories_filter_by_alias

Full suite: 174 passing (was 162), 1 warning. The +12 is the
new regression tests, no existing tests regressed.

What's still NOT canonicalized (and why)
----------------------------------------
- _rank_chunks's secondary substring boost in builder.py — the
  retriever already does the right thing via its own
  _project_match_boost which calls get_registered_project. The
  redundant secondary boost still uses the raw hint but it's a
  multiplicative factor on top of correct retrieval, not a
  filter, so it can't drop relevant chunks. Tracked as a future
  cleanup but not a P1.
- update_memory's project field (you can't change a memory's
  project after creation in the API anyway).
- The retriever's project_hint parameter on direct /query calls
  — same reasoning as the builder boost, plus the retriever's
  own get_registered_project call already handles aliases there.

src/atocore/context/builder.py

@@ -14,7 +14,7 @@ import atocore.config as _config
 from atocore.context.project_state import format_project_state, get_state
 from atocore.memory.service import get_memories_for_context
 from atocore.observability.logger import get_logger
-from atocore.projects.registry import get_registered_project
+from atocore.projects.registry import resolve_project_name
 from atocore.retrieval.retriever import ChunkResult, retrieve
 
 log = get_logger("context_builder")
@@ -85,20 +85,15 @@ def build_context(
         max(0, int(budget * PROJECT_STATE_BUDGET_RATIO)),
     )
 
-    # Resolve the project hint through the registry so callers can pass
-    # an alias (`p05`, `gigabit`) and still find trusted state stored
-    # under the canonical project id (`p05-interferometer`,
-    # `p04-gigabit`). The retriever already does this for the
-    # project-match boost — the project_state lookup needs the same
-    # courtesy. If the registry has no entry for the hint, fall back to
-    # the raw hint so a hand-curated project_state entry that predates
-    # the registry still works.
-    canonical_project = project_hint
-    if project_hint:
-        registered = get_registered_project(project_hint)
-        if registered is not None:
-            canonical_project = registered.project_id
-
+    # Canonicalize the project hint through the registry so callers
+    # can pass an alias (`p05`, `gigabit`) and still find trusted
+    # state stored under the canonical project id. The same helper
+    # is used everywhere a project name crosses a trust boundary
+    # (project_state, memories, interactions). When the registry has
+    # no entry the helper returns the input unchanged so hand-curated
+    # state that predates the registry still works.
+    canonical_project = resolve_project_name(project_hint) if project_hint else ""
+    if canonical_project:
         state_entries = get_state(canonical_project)
         if state_entries:
             project_state_text = format_project_state(state_entries)

src/atocore/context/project_state.py

@@ -18,6 +18,7 @@ from datetime import datetime, timezone
 
 from atocore.models.database import get_connection
 from atocore.observability.logger import get_logger
+from atocore.projects.registry import resolve_project_name
 
 log = get_logger("project_state")
 
@@ -101,11 +102,19 @@ def set_state(
     source: str = "",
     confidence: float = 1.0,
 ) -> ProjectStateEntry:
-    """Set or update a project state entry. Upsert semantics."""
+    """Set or update a project state entry. Upsert semantics.
+
+    The ``project_name`` is canonicalized through the registry so a
+    caller passing an alias (``p05``) ends up writing into the same
+    row as the canonical id (``p05-interferometer``). Without this
+    step, alias and canonical names would create two parallel
+    project rows and fragmented state.
+    """
     if category not in CATEGORIES:
         raise ValueError(f"Invalid category '{category}'. Must be one of: {CATEGORIES}")
     _validate_confidence(confidence)
 
+    project_name = resolve_project_name(project_name)
     project_id = ensure_project(project_name)
     entry_id = str(uuid.uuid4())
     now = datetime.now(timezone.utc).isoformat()
@@ -153,7 +162,12 @@ def get_state(
     category: str | None = None,
     active_only: bool = True,
 ) -> list[ProjectStateEntry]:
-    """Get project state entries, optionally filtered by category."""
+    """Get project state entries, optionally filtered by category.
+
+    The lookup is canonicalized through the registry so an alias hint
+    finds the same rows as the canonical id.
+    """
+    project_name = resolve_project_name(project_name)
     with get_connection() as conn:
         project = conn.execute(
             "SELECT id FROM projects WHERE lower(name) = lower(?)", (project_name,)
@@ -191,7 +205,12 @@ def get_state(
 
 
 def invalidate_state(project_name: str, category: str, key: str) -> bool:
-    """Mark a project state entry as superseded."""
+    """Mark a project state entry as superseded.
+
+    The lookup is canonicalized through the registry so an alias is
+    treated as the canonical project for the invalidation lookup.
+    """
+    project_name = resolve_project_name(project_name)
     with get_connection() as conn:
         project = conn.execute(
             "SELECT id FROM projects WHERE lower(name) = lower(?)", (project_name,)

src/atocore/interactions/service.py

@@ -18,15 +18,24 @@ violating the AtoCore trust hierarchy.
 from __future__ import annotations
 
 import json
+import re
 import uuid
 from dataclasses import dataclass, field
 from datetime import datetime, timezone
 
 from atocore.models.database import get_connection
 from atocore.observability.logger import get_logger
+from atocore.projects.registry import resolve_project_name
 
 log = get_logger("interactions")
 
+# Stored timestamps use 'YYYY-MM-DD HH:MM:SS' (no timezone offset, UTC by
+# convention) so they sort lexically and compare cleanly with the SQLite
+# CURRENT_TIMESTAMP default. The since filter accepts ISO 8601 strings
+# (with 'T', optional 'Z' or +offset, optional fractional seconds) and
+# normalizes them to the storage format before the SQL comparison.
+_STORAGE_TIMESTAMP_FORMAT = "%Y-%m-%d %H:%M:%S"
+
 
 @dataclass
 class Interaction:
@@ -72,6 +81,13 @@ def record_interaction(
     if not prompt or not prompt.strip():
         raise ValueError("Interaction prompt must be non-empty")
 
+    # Canonicalize the project through the registry so an alias and
+    # the canonical id store under the same bucket. Without this,
+    # reinforcement and extraction (which both query by raw
+    # interaction.project) would silently miss memories and create
+    # candidates in the wrong project.
+    project = resolve_project_name(project)
+
     interaction_id = str(uuid.uuid4())
     # Store created_at explicitly so the same string lives in both the DB
     # column and the returned dataclass. SQLite's CURRENT_TIMESTAMP uses
@@ -159,9 +175,14 @@ def list_interactions(
 ) -> list[Interaction]:
     """List captured interactions, optionally filtered.
 
-    ``since`` is an ISO timestamp string; only interactions created at or
-    after that time are returned. ``limit`` is hard-capped at 500 to keep
-    casual API listings cheap.
+    ``since`` accepts an ISO 8601 timestamp string (with ``T``, an
+    optional ``Z`` or numeric offset, optional fractional seconds).
+    The value is normalized to the storage format (UTC,
+    ``YYYY-MM-DD HH:MM:SS``) before the SQL comparison so external
+    callers can pass any of the common ISO shapes without filter
+    drift. ``project`` is canonicalized through the registry so an
+    alias finds rows stored under the canonical project id.
+    ``limit`` is hard-capped at 500 to keep casual API listings cheap.
     """
     if limit <= 0:
         return []
@@ -172,7 +193,7 @@ def list_interactions(
 
     if project:
         query += " AND project = ?"
-        params.append(project)
+        params.append(resolve_project_name(project))
     if session_id:
         query += " AND session_id = ?"
         params.append(session_id)
@@ -181,7 +202,7 @@ def list_interactions(
         params.append(client)
     if since:
         query += " AND created_at >= ?"
-        params.append(since)
+        params.append(_normalize_since(since))
 
     query += " ORDER BY created_at DESC LIMIT ?"
     params.append(limit)
@@ -243,3 +264,41 @@ def _safe_json_dict(raw: str | None) -> dict:
     if not isinstance(value, dict):
         return {}
     return value
+
+
+def _normalize_since(since: str) -> str:
+    """Normalize an ISO 8601 ``since`` filter to the storage format.
+
+    Stored ``created_at`` values are ``YYYY-MM-DD HH:MM:SS`` (no
+    timezone, UTC by convention). External callers naturally pass
+    ISO 8601 with ``T`` separator, optional ``Z`` suffix, optional
+    fractional seconds, and optional ``+HH:MM`` offsets. A naive
+    string comparison between the two formats fails on the same
+    day because the lexically-greater ``T`` makes any ISO value
+    sort after any space-separated value.
+
+    This helper accepts the common ISO shapes plus the bare
+    storage format and returns the storage format. On a parse
+    failure it returns the input unchanged so the SQL comparison
+    fails open (no rows match) instead of raising and breaking
+    the listing endpoint.
+    """
+    if not since:
+        return since
+    candidate = since.strip()
+    # Python's fromisoformat understands trailing 'Z' from 3.11+ but
+    # we replace it explicitly for safety against earlier shapes.
+    if candidate.endswith("Z"):
+        candidate = candidate[:-1] + "+00:00"
+    try:
+        dt = datetime.fromisoformat(candidate)
+    except ValueError:
+        # Already in storage format, or unparseable: best-effort
+        # match the storage format with a regex; if that fails too,
+        # return the raw input.
+        if re.fullmatch(r"\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}", since):
+            return since
+        return since
+    if dt.tzinfo is not None:
+        dt = dt.astimezone(timezone.utc).replace(tzinfo=None)
+    return dt.strftime(_STORAGE_TIMESTAMP_FORMAT)

src/atocore/memory/service.py

@@ -29,6 +29,7 @@ from datetime import datetime, timezone
 
 from atocore.models.database import get_connection
 from atocore.observability.logger import get_logger
+from atocore.projects.registry import resolve_project_name
 
 log = get_logger("memory")
 
@@ -84,6 +85,13 @@ def create_memory(
         raise ValueError(f"Invalid status '{status}'. Must be one of: {MEMORY_STATUSES}")
     _validate_confidence(confidence)
 
+    # Canonicalize the project through the registry so an alias and
+    # the canonical id store under the same bucket. This keeps
+    # reinforcement queries (which use the interaction's project) and
+    # context retrieval (which uses the registry-canonicalized hint)
+    # consistent with how memories are created.
+    project = resolve_project_name(project)
+
     memory_id = str(uuid.uuid4())
     now = datetime.now(timezone.utc).isoformat()
 
@@ -162,8 +170,13 @@ def get_memories(
         query += " AND memory_type = ?"
         params.append(memory_type)
     if project is not None:
+        # Canonicalize on the read side so a caller passing an alias
+        # finds rows that were stored under the canonical id (and
+        # vice versa). resolve_project_name returns the input
+        # unchanged for unregistered names so empty-string queries
+        # for "no project scope" still work.
         query += " AND project = ?"
-        params.append(project)
+        params.append(resolve_project_name(project))
     if status is not None:
         query += " AND status = ?"
         params.append(status)

src/atocore/projects/registry.py

@@ -254,6 +254,30 @@ def get_registered_project(project_name: str) -> RegisteredProject | None:
     return None
 
 
+def resolve_project_name(name: str | None) -> str:
+    """Canonicalize a project name through the registry.
+
+    Returns the canonical ``project_id`` if the input matches any
+    registered project's id or alias. Returns the input unchanged
+    when it's empty or not in the registry — the second case keeps
+    backwards compatibility with hand-curated state, memories, and
+    interactions that predate the registry, or for projects that
+    are intentionally not registered.
+
+    This helper is the single canonicalization boundary for project
+    names across the trust hierarchy. Every read/write that takes a
+    project name should pass it through ``resolve_project_name``
+    before storing or querying. The contract is documented in
+    ``docs/architecture/representation-authority.md``.
+    """
+    if not name:
+        return name or ""
+    project = get_registered_project(name)
+    if project is not None:
+        return project.project_id
+    return name
+
+
 def refresh_registered_project(project_name: str, purge_deleted: bool = False) -> dict:
     """Ingest all configured source roots for a registered project.