[dactyl] Replace every direct .decapod/data/*.db access in src/decapod/ with a dactyl::read / dactyl::write call

[alexhraber]

Summary

Once dactyl is published with the public API dactyl::read(datastore, query, optimize) / dactyl::write(datastore, query, optimize) and dactyl::init(cfg), every direct read/write of .decapod/data/*.db (and .decapod/data/*.jsonl) inside src/decapod/ must be replaced with a dactyl call.

Goal

By the end of this issue, Decapod contains no direct SQLite or HTTP-to-Neon call sites at store boundaries. Every store interaction goes through dactyl, with a universal SQL-flavored query authored at the call site and a datastore value forwarded from dactyl::active_datastore().

Call shape (authoritative)

// Per-function call site in src/decapod/
let datastore = dactyl::active_datastore();                          // "sqlite" | "neon"
let query = "select id, title, status from todos where assignee = $1"; // universal SQL-flavored
let optimize = true;                                                  // let dactyl rewrite for the active datastore
dactyl::read(datastore, query, optimize)

Notes:

• datastore MUST come from dactyl::active_datastore(). Call sites must NOT re-derive datastore from repo.effective_backend() — that translation is owned exclusively by #1112 in src/decapod/dactyl_bridge.rs. Duplicating the translation at a call site re-introduces the leak this epic exists to remove.
• The query string is authored in Decapod, per function, in universal SQL. dactyl parses it and (when optimize = true) rewrites it for the active datastore.
• For hard-coded queries, prefer dactyl::query!("select ...") so dialect/datastore mismatches are caught at compile time. optimize defaults to true inside the macro; pass optimize = false to require verbatim forward.

Scope of files to migrate

Audit src/decapod/core/ for any direct .decapod/data/*.db / *.jsonl access:

• core/db.rs
• core/broker.rs (writes broker_dedupe.db, appends broker.events.jsonl)
• core/knowledge.rs (writes knowledge.db)
• core/governance_artifacts.rs (writes governance.db)
• core/memory.rs (writes memory.db)
• core/automation.rs (writes automation.db)
• core/lcm.rs (writes lcm.db)
• core/federation.rs (reads/writes federation/_graph.json, _index.md)
• core/todo.rs (writes todo.db, appends todo.events.jsonl)
• core/flight_recorder.rs (appends traces.jsonl, verification_events.jsonl, external_actions.events.jsonl)
• core/repomap.rs if it touches data files
• any other module that opens a SQLite handle or appends to a .events.jsonl

Acceptance criteria

• grep -RIn "rusqlite\|sqlx::\|Connection::open\|\\.events\\.jsonl" src/decapod/ returns no matches outside of src/decapod/dactyl_bridge.rs (the single allowed call site that initializes dactyl and forwards backend -> datastore).
• Every store call in src/decapod/ uses the form dactyl::read(datastore, query, optimize) or dactyl::write(datastore, query, optimize), with datastore sourced from dactyl::active_datastore().
• Every query is authored in universal SQL-flavored syntax at the call site, with parameters passed alongside.
• No call site contains its own effective_backend() -> datastore translation. That logic lives only in #1112.
• decapod validate passes for both backend = "local" and backend = "cloud".
• cargo test --lib passes.

Out of scope

• Defining the dactyl crate itself → tracked in [dactyl] Bootstrap crate: unified read/write facade with both adapters (sqlite, neon) in-tree, gated by (datastore, query, optimize) dactyl#1.
• Adding missing Propodus endpoints → tracked in DecapodLabs/propodus#45–feat: add backup instructions when .bak files created #53.
• The single backend -> datastore translation point + dactyl::init(cfg) call → tracked in [dactyl] Add single backend->datastore translation point and dactyl::init(cfg) call in Decapod #1112.

Related

• Parent epic: [Epic] Backend parity: route every Decapod store through dactyl::read/dactyl::write and reach Propodus feature parity for every .decapod/data store #1110
• dactyl crate bootstrap (defines the public API this issue calls into): [dactyl] Bootstrap crate: unified read/write facade with both adapters (sqlite, neon) in-tree, gated by (datastore, query, optimize) dactyl#1
• dactyl conformance harness (proves the call sites round-trip identically): [dactyl] Conformance harness: same universal query must round-trip identically across datastore = sqlite and datastore = neon, with optimize = true and optimize = false dactyl#2
• Translation point + dactyl::init(cfg) (the one allowed place that derives datastore from backend): [dactyl] Add single backend->datastore translation point and dactyl::init(cfg) call in Decapod #1112
• Per-store Propodus endpoints: DecapodLabs/propodus#45–feat: add backup instructions when .bak files created #53

[alexhraber]

Implemented and published PR #1119 as the local SQLite architecture slice. Decapod now routes local subsystem DB paths through .decapod/data/decapod.db, namespaces shared metadata, and migrates legacy bins/files with fresh and legacy regression proof. JSONL replay compatibility remains; dactyl/Neon adapter routing is intentionally deferred until the dactyl implementation crate is available.

[alexhraber]

Note on migration call shape:
With the simplified adapter selection contract, call sites in Decapod should use the two-argument signature:
dactyl::read(query, optimize) or dactyl::write(query, optimize).
Decapod does not need to query dactyl::active_datastore() per call site, nor does it need to pass it as an argument.