bug: projects consolidate reports 'Merged: 0' without merging + mem_update does not persist project rename

[yeerliin]

Pre-flight Checks

• I have searched existing issues and this is not a duplicate
• I understand this issue needs status:approved before a PR can be opened

Bug Description

Two related bugs that cause project name fragmentation to be unrecoverable through engram's built-in tools:

Bug 1 — projects consolidate does nothing:
Running engram projects consolidate --all correctly detects groups of similar project names, but when selecting all to merge, it always reports Merged: 0 obs, 0 sessions, 0 prompts and no rows are actually updated in the database.

Bug 2 — mem_update does not persist project changes:
Calling mem_update(id, project="new_name") via MCP returns Memory updated: #ID "title" but the project column is not changed in the database. Subsequent queries still show the old project name.

Root cause of the fragmentation:
Engram MCP's mem_save normalizes project names to lowercase (e.g. Stack_Ecokey → stack_ecokey), but other code paths (CLI, older binary versions) may store the original case from the git remote. This creates duplicates like Stack_Ecokey (499 obs) and stack_ecokey (11 obs) that cannot be merged with the built-in tools.

Steps to Reproduce

1. Have a git repo with a mixed-case remote name (e.g. Stack_Ecokey)
2. Use engram across sessions — some memories end up as Stack_Ecokey, others as stack_ecokey
3. Run engram projects list — see two entries for the same project
4. Run engram projects consolidate --all and type all for the group
5. See Merged: 0 obs, 0 sessions, 0 prompts
6. Run engram projects list again — nothing changed
7. Try MCP: mem_update(id=1546, project="stack_ecokey") — returns success but project is unchanged

Expected Behavior

• projects consolidate should update all rows in sessions, observations, user_prompts, prompts_fts, sync_mutations, and observations_fts tables to the canonical project name.
• mem_update(project=...) should persist the project name change in the database.

Actual Behavior

`
$ engram projects consolidate --all
Found 2 group(s) of similar project names:

Group 2:
→ [1] Stack_Ecokey 499 obs
[2] stack_ecokey 11 obs
Suggested canonical: "Stack_Ecokey" (→)
Choice: all
Merged: 0 obs, 0 sessions, 0 prompts

$ engram projects list
Stack_Ecokey 499 obs 289 sessions 459 prompts
stack_ecokey 11 obs 6 sessions 38 prompts ← still there
`

Environment

• OS: Windows 11
• Engram Version: 1.12.0
• Agent/Client: Claude Code + OpenCode (both affected)

Workaround

Direct SQLite UPDATE against ~/.engram/engram.db:

`python
import sqlite3, shutil
from pathlib import Path

DB = Path.home() / ".engram" / "engram.db"
shutil.copy2(DB, DB.with_suffix(".db.backup"))

conn = sqlite3.connect(str(DB))
conn.execute("PRAGMA journal_mode=WAL")

TABLES = [
"sessions", "observations", "user_prompts",
"prompts_fts", "sync_mutations", "observations_fts",
]

canonical must be lowercase (engram MCP normalizes to lowercase)

MERGES = {"stack_ecokey": ["Stack_Ecokey"]}

for canonical, variants in MERGES.items():
for variant in variants:
for table in TABLES:
conn.execute(
f"UPDATE {table} SET project = ? WHERE project = ?",
(canonical, variant),
)

conn.commit()
conn.close()
`

Important: The canonical name must be lowercase because mem_save normalizes to lowercase. If you merge into the uppercase variant, fragmentation will recur on the next save.

Additional Context

• Related to feat(store): add project aliasing system to group related projects #104 (project aliasing) but this is a concrete bug in existing functionality, not a feature request.
• The fragmentation is especially common when using multiple agents (Claude Code + OpenCode) that may point to different engram binary versions with different project name detection heuristics.
• Unifying all agent configs to use the same engram binary from PATH (instead of absolute paths to different versions) prevents future fragmentation.

[jgarrone82]

Agrego contexto. He utilizado la versión 1.10.10 y encontrado el mismo error, ha persistido a través de todas esas versiones, pero en el entorno Mac el error no aparece (@Alan-TheGentleman lo ha probado en su entorno sin problemas).
En mi caso lo he analizado con la versión 1.10.10, la versión 1.11.0 y la actual, siempre con el mismo comportamiento.
Las pruebas se realizaron en dos ordenadores distintos, ambos con Windows 11 y WSL Ubuntu instalado, con diferentes proyectos.

[ismaeldouglasdev]

I'd like to fix these bugs. The project consolidate not working and mem_update not persisting project changes are important issues to resolve.