chore: apply ponytail-audit findings (9 unused deps + 11 dead functions)

[getappz]

Summary

Applies agentflare item #239's ponytail-audit findings (2026-07-21): confident, zero-risk cuts verified via ctx_callgraph (28,671-edge graph) and cargo machete.

• Removed 9 unused deps: sysinfo (+ its dead process-tree feature) and tower-http from the root crate, dirs/serde_json from agent-registry, rayon from agentflare-store's embeddings feature, chrono from flare-git-core, thiserror/tokio/tower-http from flare-proxy.
• Removed 11 zero-caller functions: doc_get_version, doc_hard_delete, try_daemon_tool_call_blocking, run_with_timeout, is_installed, clean_model, list_for_observation, init_foreground_daemon, is_foreground_daemon, needs_think_parsing, update_status, url_for — plus the now-dead imports/statics they left behind.

Two commits: deps, then dead functions.

Test plan

• cargo machete — all 9 target deps clean (remaining flags are the audit's known false positives: eyre/rpassword/bytemuck/base64/flare-docs serde)
• cargo build --workspace --all-features — clean, zero warnings
• cargo test --workspace — 773 passed, 0 failed

Summary by CodeRabbit

• Changes
  • Simplified the application’s configuration and dependency footprint.
  • Updated artifact URL handling to provide a server base URL.
  • Adjusted embedding support configuration.
  • Removed several legacy document, daemon, autostart, process, memory, and session management operations.
  • Retained existing document search, versioning, daemon, and embedding functionality where supported.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro Plus

Run ID: 57700efc-c59f-4474-8fa7-cd15276ae97c

📥 Commits

Reviewing files that changed from the base of the PR and between 41330f4 and 1e46be0.

⛔ Files ignored due to path filters (1)

• Cargo.lock is excluded by !**/*.lock

📒 Files selected for processing (15)

• Cargo.toml
• crates/agent-registry/Cargo.toml
• crates/agentflare-artifacts/src/server.rs
• crates/agentflare-store/Cargo.toml
• crates/agentflare-store/src/documents.rs
• crates/agentflare-store/src/embedding_pipeline/download.rs
• crates/flare-git-core/Cargo.toml
• crates/flare-proxy/Cargo.toml
• crates/flare-proxy/src/think.rs
• src/daemon.rs
• src/daemon_autostart.rs
• src/daemon_client.rs
• src/ipc/process.rs
• src/memory/relations.rs
• src/memory/sessions.rs

💤 Files with no reviewable changes (14)

• crates/flare-git-core/Cargo.toml
• src/daemon_autostart.rs
• crates/flare-proxy/src/think.rs
• crates/agentflare-store/src/embedding_pipeline/download.rs
• crates/agent-registry/Cargo.toml
• crates/flare-proxy/Cargo.toml
• src/memory/sessions.rs
• crates/agentflare-artifacts/src/server.rs
• src/daemon_client.rs
• crates/agentflare-store/src/documents.rs
• Cargo.toml
• src/memory/relations.rs
• src/ipc/process.rs
• src/daemon.rs

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📝 Walkthrough

Walkthrough

The pull request removes unused dependencies, features, and exported helpers across artifact serving, document storage, embedding downloads, daemon lifecycle, proxy parsing, IPC, and memory modules. It also replaces artifact-specific URL generation with a server base URL helper.

Changes

API and dependency surface pruning

Layer / File(s)	Summary
Dependency and feature cleanup Cargo.toml, crates/*/Cargo.toml	Removes unused dependencies and the process-tree feature, and changes the embeddings feature from rayon to optional ort.
Artifact and storage API changes crates/agentflare-artifacts/src/server.rs, crates/agentflare-store/src/documents.rs, crates/agentflare-store/src/embedding_pipeline/download.rs	Replaces url_for with base_url and removes document hard deletion, version lookup, and model cleanup helpers.
Daemon lifecycle API removal src/daemon.rs, src/daemon_autostart.rs, src/daemon_client.rs, src/ipc/process.rs	Removes foreground-daemon state, autostart detection, blocking daemon tool orchestration, and process timeout execution.
Memory and proxy helper removal src/memory/relations.rs, src/memory/sessions.rs, crates/flare-proxy/src/think.rs	Removes relation listing, session status updates, and model-based think-parsing detection.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Possibly related PRs

• getappz/agentflare#154: Adds the memory helpers removed from the relations and sessions modules.
• getappz/agentflare#161: Removes related legacy Engram integration components.
• getappz/agentflare#271: Adds daemon and IPC helpers removed by this pull request.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly summarizes the main change: removing unused dependencies and dead functions from the workspace.
Description check	✅ Passed	The description covers Summary and Test plan well, but it omits the Notes for reviewers section from the template.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch task/239

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