feat(logging): structured logging via tracing across all binaries

AGENTS.md

@@ -69,6 +69,7 @@ Large-diff work is a separate evaluation track, not part of the default live-rep
 - **LLM-as-judge** — evaluator that scores analysis quality across 5 criteria
 - **Eval suite** — 5 synthetic fixture codebases, deterministic scoring, 0.89 avg score
 - **Config** — `.diffcore.toml` with entrypoint globs, layer names, ignore patterns, LLM settings, refinement settings
+- **Logging** — `tracing` + `tracing-subscriber` behind `diffcore-core`'s `logging` feature; `RUST_LOG` sets the filter (default `info`), `DIFFCORE_LOG_FORMAT=json` switches to line-delimited JSON, `DIFFCORE_LOG_FILE` redirects to a file (the desktop app falls back to `~/.diffcore/desktop.log` when stderr is not a terminal, since GUI bundles discard it). Backend activity logs on the `activity` target, IR cache on `ir_cache`. `log`-crate call sites bridge in automatically.
 
 ## Tests
 

Cargo.toml

@@ -14,6 +14,8 @@ serde = { version = "1", features = ["derive"] }
 # stable for arbitrary f64 scores (see assert_json_roundtrip).
 serde_json = { version = "1", features = ["float_roundtrip"] }
 log = "0.4"
+tracing = "0.1"
+tracing-subscriber = { version = "0.3", features = ["env-filter", "json"] }
 git2 = { version = "0.20", default-features = false }
 
 # Optimize test builds: trades slightly longer compile for faster test runtime.

README.md

@@ -199,6 +199,24 @@ When using direct API providers (`anthropic`, `openai`, `gemini`), Diffcore chec
 
 When using `codex` or `claude`, Diffcore uses the local CLI login instead of an API key and lets that agent inspect the repository with structured output constraints.
 
+### Logging
+
+`diffcore` and `diffcore-web` log to stderr at `info` by default, so piping
+stdout to `jq` still works; the desktop app logs to a file (see below).
+
+Backend activity (`codex`, `claude`) logs on the `activity` target with `source`
+and `event_type` fields — the same events the desktop UI shows; the IR cache logs
+on `ir_cache`.
+
+```bash
+RUST_LOG=info,activity=warn diffcore analyze --base main   # mute per-event chatter
+DIFFCORE_LOG_FORMAT=json diffcore analyze --base main 2> analyze.log.jsonl
+```
+
+Launched from a terminal the desktop app logs there like the others; launched
+from Finder or a `.desktop` entry — where stderr is discarded — it falls back to
+`~/.diffcore/desktop.log`. `DIFFCORE_LOG_FILE` overrides the path for any binary.
+
 ## Architecture
 
 ```

crates/diffcore-cli/Cargo.toml

@@ -8,14 +8,13 @@ name = "diffcore"
 path = "src/main.rs"
 
 [dependencies]
-diffcore-core = { path = "../diffcore-core" }
+diffcore-core = { path = "../diffcore-core", features = ["logging"] }
 clap = { version = "4", features = ["derive"] }
 serde_json = { workspace = true }
 git2 = { workspace = true }
 tokio = { version = "1", features = ["full"] }
 tempfile = "3"
 log = { workspace = true }
-env_logger = "0.11"
 
 [features]
 embeddings = ["diffcore-core/embeddings"]

crates/diffcore-cli/src/main.rs

@@ -272,7 +272,7 @@ struct EmbedDiffArgs {
 }
 
 fn main() {
-    env_logger::init();
+    diffcore_core::logging::init(None);
     let cli = Cli::parse();
 
     match cli.command {
@@ -697,7 +697,7 @@ async fn run_refinement(
     );
 
     for w in &warnings {
-        eprintln!("refinement repair: {}", w.message);
+        warn!(target: "refinement", "repair: {}", w.message);
     }
 
     analysis_output.groups = refined_groups;

crates/diffcore-core/Cargo.toml

@@ -30,6 +30,8 @@ bincode = "1"
 dashmap = "6"
 once_cell = "1"
 log = { workspace = true }
+tracing = { workspace = true }
+tracing-subscriber = { workspace = true, optional = true }
 tempfile = "3"
 tree-sitter-c-sharp = "0.23.1"
 tree-sitter-php = "0.24.2"
@@ -48,12 +50,14 @@ test-support = []
 ## Enables local code embeddings via fastembed (ONNX Runtime + Jina Code model).
 ## Used for semantic similarity between file diffs in clustering.
 embeddings = ["dep:fastembed"]
+## Subscriber stack for the binaries; library consumers skip it.
+logging = ["dep:tracing-subscriber"]
 
 # Enable test-support feature automatically when running tests
 # (dev-dependencies trigger `cfg(test)` in unit tests but not integration tests,
 # so we also enable the feature here for integration test access to `with_base_url`).
 [dev-dependencies]
-diffcore-core = { path = ".", features = ["test-support"] }
+diffcore-core = { path = ".", features = ["test-support", "logging"] }
 proptest = "1"
 tokio = { version = "1", features = ["full", "test-util"] }
 wiremock = "0.6"