fix: resolve working_directory relative to config file, not CWD

When running `codspeed run` with config targets, the `working-directory`
option is now resolved relative to the config file's directory instead
of the current working directory. When no `working-directory` is set,
it defaults to the config file's directory.

For `codspeed run -- command` and `codspeed exec`, the config's
`working-directory` is explicitly ignored — only the `--working-directory`
CLI flag is used. A warning is emitted if `--working-directory` is passed
in config targets mode.

Author: GuillaumeLagrange

Cargo.lock

@@ -84,6 +84,8 @@ test-with = { version = "0.15", default-features = false, features = [] }
 rstest = { version = "0.25.0", default-features = false }
 rstest_reuse = "0.7.0"
 shell-quote = "0.7.2"
+assert_cmd = "2.0.16"
+predicates = "3.1.4"
 
 [workspace]
 members = [

Cargo.toml

@@ -40,10 +40,6 @@ impl ExecArgs {
     /// CLI arguments take precedence over config values.
     pub fn merge_with_project_config(mut self, project_config: Option<&ProjectConfig>) -> Self {
         if let Some(project_config) = project_config {
-            // Merge shared args
-            self.shared =
-                ConfigMerger::merge_shared_args(&self.shared, project_config.options.as_ref());
-            // Merge walltime args
             self.walltime_args = ConfigMerger::merge_walltime_options(
                 &self.walltime_args,
                 project_config

src/cli/exec/mod.rs

@@ -5,8 +5,7 @@ use crate::executor;
 use crate::executor::config::{self, OrchestratorConfig, RepositoryOverride};
 use crate::instruments::Instruments;
 use crate::prelude::*;
-use crate::project_config::merger::ConfigMerger;
-use crate::project_config::{DiscoveredProjectConfig, ProjectConfig};
+use crate::project_config::DiscoveredProjectConfig;
 use crate::run_environment::interfaces::RepositoryProvider;
 use crate::upload::poll_results::PollResultsOptions;
 use clap::{Args, ValueEnum};
@@ -40,19 +39,6 @@ pub struct RunArgs {
     pub command: Vec<String>,
 }
 
-impl RunArgs {
-    /// Merge CLI args with project config if available
-    ///
-    /// CLI arguments take precedence over config values.
-    pub fn merge_with_project_config(mut self, project_config: Option<&ProjectConfig>) -> Self {
-        if let Some(project_config) = project_config {
-            self.shared =
-                ConfigMerger::merge_shared_args(&self.shared, project_config.options.as_ref());
-        }
-        self
-    }
-}
-
 #[derive(ValueEnum, Clone, Debug, PartialEq)]
 pub enum MessageFormat {
     Json,
@@ -158,7 +144,6 @@ pub async fn run(
     let output_json = args.message_format == Some(MessageFormat::Json);
     let project_config = discovered_config.map(|d| &d.config);
 
-    let args = args.merge_with_project_config(project_config);
     let run_target = if args.command.is_empty() {
         // No command provided - check for targets in project config
         let targets = project_config
@@ -183,6 +168,8 @@ pub async fn run(
 
     match run_target {
         RunTarget::SingleCommand(args) => {
+            // SingleCommand: working_directory comes from --working-directory CLI flag only.
+            // Config file's working-directory is NOT used.
             let command = args.command.join(" ");
             let config = build_orchestrator_config(
                 args,
@@ -192,6 +179,7 @@ pub async fn run(
                 }],
                 PollResultsOptions::for_run(output_json),
             )?;
+
             let orchestrator =
                 executor::Orchestrator::new(config, codspeed_config, api_client).await?;
 
@@ -208,10 +196,44 @@ pub async fn run(
             targets,
             default_walltime,
         } => {
+            // ConfigTargets: working_directory is resolved relative to config file dir.
+            // If --working-directory CLI flag is passed, ignore it with a warning.
+            if args.shared.working_directory.is_some() {
+                // Intentionally using eprintln! because logger has not been initialized yet.
+                eprintln!(
+                    "Warning: The --working-directory flag is ignored when running targets from the config file. \
+                    Use the `working-directory` option in the config file instead."
+                );
+            }
+
+            // Resolve working_directory relative to config file directory
+            let resolved_working_directory =
+                if let Some(config_dir) = discovered_config.and_then(|d| d.config_dir()) {
+                    let root_wd = project_config
+                        .and_then(|c| c.options.as_ref())
+                        .and_then(|o| o.working_directory.as_ref());
+
+                    match root_wd {
+                        Some(wd) => {
+                            let wd_path = Path::new(wd);
+                            if wd_path.is_absolute() {
+                                Some(wd.clone())
+                            } else {
+                                Some(config_dir.join(wd).to_string_lossy().into_owned())
+                            }
+                        }
+                        None => Some(config_dir.to_string_lossy().into_owned()),
+                    }
+                } else {
+                    None
+                };
+
             let benchmark_targets =
                 super::exec::multi_targets::build_benchmark_targets(targets, default_walltime)?;
-            let config =
+            let mut config =
                 build_orchestrator_config(args, benchmark_targets, PollResultsOptions::for_exec())?;
+            config.working_directory = resolved_working_directory;
+
             super::exec::execute_config(config, api_client, codspeed_config, setup_cache_dir)
                 .await?;
         }

src/cli/run/mod.rs

@@ -13,7 +13,6 @@ const CONFIG_FILENAMES: &[&str] = &[
 
 /// A project configuration paired with the path it was loaded from.
 #[derive(Debug)]
-#[allow(dead_code)]
 pub struct DiscoveredProjectConfig {
     pub config: ProjectConfig,
     pub path: PathBuf,
@@ -64,7 +63,6 @@ impl DiscoveredProjectConfig {
     }
 
     /// Returns the directory containing the config file.
-    #[allow(dead_code)]
     pub fn config_dir(&self) -> Option<PathBuf> {
         let canonical_path = self
             .path

src/project_config/discover.rs

@@ -1,7 +1,6 @@
-use crate::cli::ExecAndRunSharedArgs;
 use exec_harness::walltime::WalltimeExecutionArgs;
 
-use super::{ProjectOptions, WalltimeOptions};
+use super::WalltimeOptions;
 
 /// Handles merging of CLI arguments with project configuration
 ///
@@ -35,20 +34,6 @@ impl ConfigMerger {
         }
     }
 
-    /// Merge shared args with project config options
-    ///
-    /// CLI arguments take precedence over config values.
-    /// Note: Some fields like upload_url, token, repository are CLI-only and not in config.
-    pub fn merge_shared_args(
-        cli: &ExecAndRunSharedArgs,
-        _config_opts: Option<&ProjectOptions>,
-    ) -> ExecAndRunSharedArgs {
-        // Note: working_directory is NOT merged here because config paths need to be
-        // resolved relative to the config file directory. This resolution is handled
-        // by the caller (e.g., `codspeed run`) which has access to the config file path.
-        cli.clone()
-    }
-
     /// Helper to merge Option values with precedence: CLI > config > None
     fn merge_option<T: Clone>(cli_value: &Option<T>, config_value: Option<&T>) -> Option<T> {
         cli_value.clone().or_else(|| config_value.cloned())
@@ -58,31 +43,6 @@ impl ConfigMerger {
 #[cfg(test)]
 mod tests {
     use super::*;
-    use crate::cli::PerfRunArgs;
-    use crate::runner_mode::RunnerMode;
-
-    fn make_cli(working_directory: Option<&str>) -> ExecAndRunSharedArgs {
-        ExecAndRunSharedArgs {
-            upload_url: None,
-            token: None,
-            repository: None,
-            provider: None,
-            working_directory: working_directory.map(|s| s.to_string()),
-            mode: vec![RunnerMode::Walltime],
-            simulation_tool: None,
-            profile_folder: None,
-            skip_upload: false,
-            skip_run: false,
-            skip_setup: false,
-            allow_empty: false,
-            go_runner_version: None,
-            show_full_output: false,
-            perf_run_args: PerfRunArgs {
-                enable_perf: true,
-                perf_unwinding_mode: None,
-            },
-        }
-    }
 
     #[test]
     fn test_merge_walltime_all_from_cli() {
@@ -161,47 +121,6 @@ mod tests {
         assert_eq!(merged.min_rounds, None);
     }
 
-    #[test]
-    fn test_merge_shared_args_working_directory_from_cli() {
-        let cli = make_cli(Some("./cli-dir"));
-        let config = ProjectOptions {
-            walltime: None,
-            working_directory: Some("./config-dir".to_string()),
-        };
-
-        let merged = ConfigMerger::merge_shared_args(&cli, Some(&config));
-
-        // CLI working_directory should win
-        assert_eq!(merged.working_directory, Some("./cli-dir".to_string()));
-    }
-
-    #[test]
-    fn test_merge_shared_args_working_directory_not_merged_from_config() {
-        let cli = make_cli(None);
-        let config = ProjectOptions {
-            walltime: None,
-            working_directory: Some("./config-dir".to_string()),
-        };
-
-        let merged = ConfigMerger::merge_shared_args(&cli, Some(&config));
-
-        // Config working_directory is NOT merged — resolution is handled by the caller
-        // relative to the config file directory.
-        assert_eq!(merged.working_directory, None);
-        // Mode stays as CLI value
-        assert_eq!(merged.mode, vec![RunnerMode::Walltime]);
-    }
-
-    #[test]
-    fn test_merge_shared_args_no_config() {
-        let cli = make_cli(Some("./dir"));
-
-        let merged = ConfigMerger::merge_shared_args(&cli, None);
-
-        // Should be identical to CLI
-        assert_eq!(merged.working_directory, Some("./dir".to_string()));
-    }
-
     #[test]
     fn test_merge_option_helper() {
         // CLI value wins