feat: enhance skills downloading and proxy configuration

apps/desktop/src-tauri/Cargo.lock

@@ -2172,9 +2172,11 @@ dependencies = [
  "percent-encoding",
  "pin-project-lite",
  "socket2 0.5.10",
+ "system-configuration 0.7.0",
  "tokio",
  "tower-service",
  "tracing",
+ "windows-registry",
 ]
 
 [[package]]
@@ -4054,7 +4056,7 @@ dependencies = [
  "serde_json",
  "serde_urlencoded",
  "sync_wrapper 0.1.2",
- "system-configuration",
+ "system-configuration 0.5.1",
  "tokio",
  "tokio-native-tls",
  "tower-service",
@@ -4968,7 +4970,18 @@ checksum = "ba3a3adc5c275d719af8cb4272ea1c4a6d668a777f37e115f6d11ddbc1c8e0e7"
 dependencies = [
  "bitflags 1.3.2",
  "core-foundation 0.9.4",
- "system-configuration-sys",
+ "system-configuration-sys 0.5.0",
+]
+
+[[package]]
+name = "system-configuration"
+version = "0.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a13f3d0daba03132c0aa9767f98351b3488edc2c100cda2d2ec2b04f3d8d3c8b"
+dependencies = [
+ "bitflags 2.13.0",
+ "core-foundation 0.9.4",
+ "system-configuration-sys 0.6.0",
 ]
 
 [[package]]
@@ -4981,6 +4994,16 @@ dependencies = [
  "libc",
 ]
 
+[[package]]
+name = "system-configuration-sys"
+version = "0.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8e1d1b10ced5ca923a1fcb8d03e96b8d3268065d724548c0211415ff6ac6bac4"
+dependencies = [
+ "core-foundation-sys",
+ "libc",
+]
+
 [[package]]
 name = "system-deps"
 version = "6.2.2"
@@ -6876,8 +6899,8 @@ dependencies = [
  "windows-implement",
  "windows-interface",
  "windows-link 0.1.3",
- "windows-result",
- "windows-strings",
+ "windows-result 0.3.4",
+ "windows-strings 0.4.2",
 ]
 
 [[package]]
@@ -6935,6 +6958,17 @@ dependencies = [
  "windows-link 0.1.3",
 ]
 
+[[package]]
+name = "windows-registry"
+version = "0.6.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "02752bf7fbdcce7f2a27a742f798510f3e5ad88dbe84871e5168e2120c3d5720"
+dependencies = [
+ "windows-link 0.2.1",
+ "windows-result 0.4.1",
+ "windows-strings 0.5.1",
+]
+
 [[package]]
 name = "windows-result"
 version = "0.3.4"
@@ -6944,6 +6978,15 @@ dependencies = [
  "windows-link 0.1.3",
 ]
 
+[[package]]
+name = "windows-result"
+version = "0.4.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7781fa89eaf60850ac3d2da7af8e5242a5ea78d1a11c49bf2910bb5a73853eb5"
+dependencies = [
+ "windows-link 0.2.1",
+]
+
 [[package]]
 name = "windows-strings"
 version = "0.4.2"
@@ -6953,6 +6996,15 @@ dependencies = [
  "windows-link 0.1.3",
 ]
 
+[[package]]
+name = "windows-strings"
+version = "0.5.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7837d08f69c77cf6b07689544538e017c1bfcf57e34b4c0ff58e6c2cd3b37091"
+dependencies = [
+ "windows-link 0.2.1",
+]
+
 [[package]]
 name = "windows-sys"
 version = "0.45.0"

apps/desktop/src-tauri/Cargo.toml

@@ -23,7 +23,7 @@ serde_json = "1"
 serde_yaml = "0.9"
 tokio = { version = "1", features = ["full"] }
 dirs = "5"
-reqwest = { version = "0.12", default-features = false, features = ["rustls-tls", "stream"] }
+reqwest = { version = "0.12", default-features = false, features = ["rustls-tls", "stream", "system-proxy", "socks"] }
 hmac = "0.12"
 sha1 = "0.10"
 base64 = "0.22"

apps/desktop/src-tauri/src/skills.rs

@@ -1,12 +1,18 @@
 use serde::{Deserialize, Serialize};
 use std::path::{Path, PathBuf};
+use std::time::Duration;
 use tauri::{Emitter, Manager, WebviewWindow};
 
-const TARBALL_URL: &str =
-    "https://github.com/K-Dense-AI/scientific-agent-skills/archive/refs/heads/main.tar.gz";
-const SKILLS_DOWNLOAD_TIMEOUT_SECS: u64 = 120;
+const TARBALL_URLS: &[&str] = &[
+    "https://github.com/K-Dense-AI/scientific-agent-skills/archive/refs/heads/main.tar.gz",
+    "https://codeload.github.com/K-Dense-AI/scientific-agent-skills/tar.gz/refs/heads/main",
+    "https://github.com/K-Dense-AI/claude-scientific-skills/archive/refs/heads/main.tar.gz",
+];
+const SKILLS_DOWNLOAD_ATTEMPTS: usize = 3;
+const SKILLS_DOWNLOAD_TIMEOUT_SECS: u64 = 240;
 const SKILLS_CONNECT_TIMEOUT_SECS: u64 = 20;
-const SKILLS_INSTALL_TIMEOUT_SECS: u64 = 180;
+const SKILLS_INSTALL_TIMEOUT_SECS: u64 = 420;
+const SKILL_CONTENT_TIMEOUT_SECS: u64 = 45;
 const RAW_SKILL_URLS: &[&str] = &[
     "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/main/skills",
     "https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/main/scientific-skills",
@@ -423,24 +429,404 @@ fn collect_skill_dirs(root: &Path, output: &mut Vec<PathBuf>) {
     }
 }
 
-/// Download and extract tarball.
-async fn download_tarball(window: &WebviewWindow, tmp_dir: &Path) -> Result<(), String> {
-    let client = reqwest::Client::builder()
-        .connect_timeout(std::time::Duration::from_secs(SKILLS_CONNECT_TIMEOUT_SECS))
-        .timeout(std::time::Duration::from_secs(SKILLS_DOWNLOAD_TIMEOUT_SECS))
+#[derive(Clone, Copy, Debug, PartialEq, Eq)]
+enum ProxyKind {
+    All,
+    Http,
+    Https,
+}
+
+struct ProxyRule {
+    kind: ProxyKind,
+    url: String,
+    source: String,
+}
+
+fn first_env_value(names: &[&str]) -> Option<(String, String)> {
+    for name in names {
+        let Ok(value) = std::env::var(name) else {
+            continue;
+        };
+        let trimmed = value.trim();
+        if !trimmed.is_empty() {
+            return Some(((*name).to_string(), trimmed.to_string()));
+        }
+    }
+
+    None
+}
+
+fn normalize_proxy_url(raw: &str) -> Option<String> {
+    normalize_proxy_url_with_default(raw, "http")
+}
+
+fn normalize_proxy_url_with_default(raw: &str, default_scheme: &str) -> Option<String> {
+    let trimmed = raw.trim();
+    if trimmed.is_empty() {
+        return None;
+    }
+
+    if trimmed.contains("://") {
+        Some(trimmed.to_string())
+    } else {
+        Some(format!("{}://{}", default_scheme, trimmed))
+    }
+}
+
+fn explicit_env_proxy_rules() -> Vec<ProxyRule> {
+    let mut rules = Vec::new();
+    let mut has_https_proxy = false;
+    let mut has_all_proxy = false;
+    let mut http_proxy = None;
+
+    if let Some((source, raw)) = first_env_value(&["HTTPS_PROXY", "https_proxy"]) {
+        if let Some(url) = normalize_proxy_url(&raw) {
+            rules.push(ProxyRule {
+                kind: ProxyKind::Https,
+                url,
+                source,
+            });
+            has_https_proxy = true;
+        }
+    }
+
+    if let Some((source, raw)) = first_env_value(&["HTTP_PROXY", "http_proxy"]) {
+        if let Some(url) = normalize_proxy_url(&raw) {
+            http_proxy = Some((source.clone(), url.clone()));
+            rules.push(ProxyRule {
+                kind: ProxyKind::Http,
+                url,
+                source,
+            });
+        }
+    }
+
+    if let Some((source, raw)) = first_env_value(&["ALL_PROXY", "all_proxy"]) {
+        if let Some(url) = normalize_proxy_url(&raw) {
+            rules.push(ProxyRule {
+                kind: ProxyKind::All,
+                url,
+                source,
+            });
+            has_all_proxy = true;
+        }
+    }
+
+    if !has_https_proxy && !has_all_proxy {
+        if let Some((source, url)) = http_proxy {
+            rules.insert(
+                0,
+                ProxyRule {
+                    kind: ProxyKind::Https,
+                    url,
+                    source: format!("{} (HTTPS fallback)", source),
+                },
+            );
+        }
+    }
+
+    rules
+}
+
+#[cfg(target_os = "windows")]
+fn windows_proxy_override_to_no_proxy(raw: &str) -> Option<reqwest::NoProxy> {
+    let entries = raw
+        .split([';', ','])
+        .filter_map(|part| {
+            let trimmed = part.trim();
+            if trimmed.is_empty() {
+                return None;
+            }
+
+            if trimmed.eq_ignore_ascii_case("<local>") {
+                return Some("localhost,127.0.0.1,::1".to_string());
+            }
+
+            if trimmed == "*" {
+                return Some(trimmed.to_string());
+            }
+
+            if trimmed.contains('*') {
+                return trimmed
+                    .strip_prefix("*.")
+                    .map(|domain| format!(".{}", domain.trim_start_matches('.')));
+            }
+
+            Some(trimmed.to_string())
+        })
+        .collect::<Vec<_>>();
+
+    if entries.is_empty() {
+        None
+    } else {
+        reqwest::NoProxy::from_string(&entries.join(","))
+    }
+}
+
+#[cfg(target_os = "windows")]
+fn windows_system_no_proxy() -> Option<reqwest::NoProxy> {
+    use winreg::enums::HKEY_CURRENT_USER;
+    use winreg::RegKey;
+
+    let settings = RegKey::predef(HKEY_CURRENT_USER)
+        .open_subkey(r"Software\Microsoft\Windows\CurrentVersion\Internet Settings")
+        .ok()?;
+    let raw = settings.get_value::<String, _>("ProxyOverride").ok()?;
+    windows_proxy_override_to_no_proxy(&raw)
+}
+
+#[cfg(target_os = "windows")]
+fn parse_windows_proxy_server(raw: &str) -> Vec<ProxyRule> {
+    let trimmed = raw.trim();
+    if trimmed.is_empty() {
+        return Vec::new();
+    }
+
+    if !trimmed.contains('=') {
+        return normalize_proxy_url(trimmed)
+            .map(|url| {
+                vec![ProxyRule {
+                    kind: ProxyKind::All,
+                    url,
+                    source: "Windows system proxy".to_string(),
+                }]
+            })
+            .unwrap_or_default();
+    }
+
+    let mut rules = Vec::new();
+    for entry in trimmed.split(';') {
+        let Some((scheme, value)) = entry.split_once('=') else {
+            continue;
+        };
+        let scheme = scheme.trim();
+        let (kind, default_proxy_scheme) = match scheme.to_ascii_lowercase().as_str() {
+            "http" => (ProxyKind::Http, "http"),
+            "https" => (ProxyKind::Https, "http"),
+            "socks" | "socks5" => (ProxyKind::All, "socks5"),
+            "socks4" => (ProxyKind::All, "socks4"),
+            _ => continue,
+        };
+        let Some(url) = normalize_proxy_url_with_default(value, default_proxy_scheme) else {
+            continue;
+        };
+
+        rules.push(ProxyRule {
+            kind,
+            url,
+            source: format!("Windows system proxy ({})", scheme.trim()),
+        });
+    }
+
+    rules
+}
+
+#[cfg(target_os = "windows")]
+fn windows_system_proxy_rules() -> Vec<ProxyRule> {
+    use winreg::enums::HKEY_CURRENT_USER;
+    use winreg::RegKey;
+
+    let Ok(settings) = RegKey::predef(HKEY_CURRENT_USER)
+        .open_subkey(r"Software\Microsoft\Windows\CurrentVersion\Internet Settings")
+    else {
+        return Vec::new();
+    };
+
+    let proxy_enabled = settings.get_value::<u32, _>("ProxyEnable").unwrap_or(0) != 0;
+    if !proxy_enabled {
+        return Vec::new();
+    }
+
+    settings
+        .get_value::<String, _>("ProxyServer")
+        .map(|raw| parse_windows_proxy_server(&raw))
+        .unwrap_or_default()
+}
+
+#[cfg(not(target_os = "windows"))]
+fn windows_system_proxy_rules() -> Vec<ProxyRule> {
+    Vec::new()
+}
+
+#[cfg(not(target_os = "windows"))]
+fn windows_system_no_proxy() -> Option<reqwest::NoProxy> {
+    None
+}
+
+fn redacted_proxy_url(url: &str) -> String {
+    let Ok(mut parsed) = reqwest::Url::parse(url) else {
+        return "<invalid proxy URL>".to_string();
+    };
+
+    if !parsed.username().is_empty() {
+        let _ = parsed.set_username("***");
+        if parsed.password().is_some() {
+            let _ = parsed.set_password(Some("***"));
+        }
+    }
+
+    parsed.to_string()
+}
+
+fn add_proxy_rule(
+    builder: reqwest::ClientBuilder,
+    rule: &ProxyRule,
+    no_proxy: Option<reqwest::NoProxy>,
+) -> Result<reqwest::ClientBuilder, String> {
+    let proxy = match rule.kind {
+        ProxyKind::All => reqwest::Proxy::all(&rule.url),
+        ProxyKind::Http => reqwest::Proxy::http(&rule.url),
+        ProxyKind::Https => reqwest::Proxy::https(&rule.url),
+    }
+    .map_err(|e| {
+        format!(
+            "Invalid proxy from {} ({}): {}",
+            rule.source,
+            redacted_proxy_url(&rule.url),
+            e
+        )
+    })?;
+
+    let proxy = proxy.no_proxy(no_proxy);
+    Ok(builder.proxy(proxy))
+}
+
+fn configure_proxy_for_client(
+    mut builder: reqwest::ClientBuilder,
+    window: Option<&WebviewWindow>,
+) -> Result<reqwest::ClientBuilder, String> {
+    let mut rules = explicit_env_proxy_rules();
+    let mut no_proxy = reqwest::NoProxy::from_env();
+
+    if rules.is_empty() {
+        let windows_rules = windows_system_proxy_rules();
+        if !windows_rules.is_empty() {
+            rules = windows_rules;
+            no_proxy = windows_system_no_proxy();
+        }
+    }
+
+    if rules.is_empty() {
+        if let Some(window) = window {
+            emit_log(window, "Using system proxy settings when available");
+        }
+        return Ok(builder);
+    }
+
+    if let Some(window) = window {
+        for rule in &rules {
+            emit_log(
+                window,
+                &format!(
+                    "Using proxy from {}: {}",
+                    rule.source,
+                    redacted_proxy_url(&rule.url)
+                ),
+            );
+        }
+    }
+
+    for rule in &rules {
+        builder = add_proxy_rule(builder, rule, no_proxy.clone())?;
+    }
+
+    Ok(builder)
+}
+
+fn build_skills_http_client(
+    timeout_secs: u64,
+    window: Option<&WebviewWindow>,
+) -> Result<reqwest::Client, String> {
+    let builder = reqwest::Client::builder()
+        .connect_timeout(Duration::from_secs(SKILLS_CONNECT_TIMEOUT_SECS))
+        .timeout(Duration::from_secs(timeout_secs));
+
+    configure_proxy_for_client(builder, window)?
         .build()
-        .map_err(|e| format!("Failed to create download client: {}", e))?;
+        .map_err(|e| format!("Failed to create download client: {}", e))
+}
+
+fn tarball_source_label(url: &str) -> &'static str {
+    if url.contains("codeload.github.com") {
+        "GitHub codeload"
+    } else if url.contains("claude-scientific-skills") {
+        "legacy GitHub archive"
+    } else {
+        "GitHub archive"
+    }
+}
+
+fn reset_download_workspace(tmp_dir: &Path) {
+    let _ = std::fs::remove_dir_all(tmp_dir.join("repo"));
+    let _ = std::fs::remove_dir_all(tmp_dir.join("repo-raw"));
+}
+
+fn find_extracted_repo_dir(raw_dir: &Path) -> Option<PathBuf> {
+    let mut candidates = Vec::new();
+    let entries = std::fs::read_dir(raw_dir).ok()?;
+
+    for entry in entries.flatten() {
+        let path = entry.path();
+        if path.is_dir() {
+            candidates.push(path);
+        }
+    }
+    candidates.sort();
+
+    for candidate in &candidates {
+        if find_skills_source(candidate).is_some() {
+            return Some(candidate.clone());
+        }
+    }
+
+    candidates.into_iter().next()
+}
+
+fn unpack_tarball(bytes: &[u8], tmp_dir: &Path) -> Result<(), String> {
+    reset_download_workspace(tmp_dir);
+
+    let raw_dir = tmp_dir.join("repo-raw");
+    std::fs::create_dir_all(&raw_dir)
+        .map_err(|e| format!("Failed to create extraction dir: {}", e))?;
+
+    let decoder = flate2::read::GzDecoder::new(bytes);
+    let mut archive = tar::Archive::new(decoder);
+
+    archive
+        .unpack(&raw_dir)
+        .map_err(|e| format!("Failed to extract tarball: {}", e))?;
+
+    let repo_source = find_extracted_repo_dir(&raw_dir)
+        .ok_or_else(|| "Downloaded tarball did not contain a repository directory".to_string())?;
+
+    std::fs::rename(&repo_source, tmp_dir.join("repo"))
+        .map_err(|e| format!("Failed to prepare extracted repo: {}", e))?;
+
+    let _ = std::fs::remove_dir_all(&raw_dir);
+    Ok(())
+}
+
+async fn download_tarball_once(
+    client: &reqwest::Client,
+    window: &WebviewWindow,
+    tmp_dir: &Path,
+    url: &str,
+) -> Result<(), String> {
+    reset_download_workspace(tmp_dir);
+
+    let source_label = tarball_source_label(url);
+    emit_log(window, &format!("Downloading from {}...", source_label));
 
     let mut response = client
-        .get(TARBALL_URL)
+        .get(url)
         .header(reqwest::header::USER_AGENT, "ClaudePrism skills installer")
         .send()
         .await
-        .map_err(|e| format!("Failed to download tarball: {}", e))?;
+        .map_err(|e| format!("Failed to start download: {}", e))?;
 
     if !response.status().is_success() {
         return Err(format!(
-            "Tarball download failed with status: {}",
+            "Download failed with status: {}",
             response.status()
         ));
     }
@@ -454,7 +840,7 @@ async fn download_tarball(window: &WebviewWindow, tmp_dir: &Path) -> Result<(),
     while let Some(chunk) = response
         .chunk()
         .await
-        .map_err(|e| format!("Failed to read tarball bytes: {}", e))?
+        .map_err(|e| format!("Failed to read download bytes: {}", e))?
     {
         downloaded += chunk.len() as u64;
         bytes.extend_from_slice(&chunk);
@@ -473,28 +859,48 @@ async fn download_tarball(window: &WebviewWindow, tmp_dir: &Path) -> Result<(),
         }
     }
 
-    // Decompress gzip
-    let decoder = flate2::read::GzDecoder::new(&bytes[..]);
-    let mut archive = tar::Archive::new(decoder);
+    unpack_tarball(&bytes, tmp_dir)
+}
 
-    archive
-        .unpack(tmp_dir.join("repo-raw"))
-        .map_err(|e| format!("Failed to extract tarball: {}", e))?;
+/// Download and extract tarball.
+async fn download_tarball(window: &WebviewWindow, tmp_dir: &Path) -> Result<(), String> {
+    let client = build_skills_http_client(SKILLS_DOWNLOAD_TIMEOUT_SECS, Some(window))?;
 
-    // The tarball extracts to scientific-agent-skills-main/
-    // We need to find it and rename to repo/
-    let raw_dir = tmp_dir.join("repo-raw");
-    if let Ok(mut entries) = std::fs::read_dir(&raw_dir) {
-        if let Some(Ok(entry)) = entries.next() {
-            std::fs::rename(entry.path(), tmp_dir.join("repo"))
-                .map_err(|e| format!("Failed to rename extracted dir: {}", e))?;
+    let mut last_error = None;
+    for attempt in 1..=SKILLS_DOWNLOAD_ATTEMPTS {
+        for url in TARBALL_URLS {
+            let label = tarball_source_label(url);
+            emit_log(
+                window,
+                &format!(
+                    "Download attempt {}/{} ({})",
+                    attempt, SKILLS_DOWNLOAD_ATTEMPTS, label
+                ),
+            );
+
+            match download_tarball_once(&client, window, tmp_dir, url).await {
+                Ok(()) => return Ok(()),
+                Err(e) => {
+                    let message = format!("{} failed: {}", label, e);
+                    emit_log(window, &message);
+                    last_error = Some(message);
+                    reset_download_workspace(tmp_dir);
+                }
+            }
+        }
+
+        if attempt < SKILLS_DOWNLOAD_ATTEMPTS {
+            let delay_secs = attempt as u64 * 2;
+            emit_log(window, &format!("Retrying in {} seconds...", delay_secs));
+            tokio::time::sleep(Duration::from_secs(delay_secs)).await;
         }
     }
 
-    // Clean up the raw extraction directory
-    let _ = std::fs::remove_dir_all(&raw_dir);
-
-    Ok(())
+    Err(format!(
+        "Failed to download skills after {} attempts. Last error: {}",
+        SKILLS_DOWNLOAD_ATTEMPTS,
+        last_error.unwrap_or_else(|| "unknown download error".to_string())
+    ))
 }
 
 fn contains_skill_dirs(path: &Path) -> bool {
@@ -526,6 +932,81 @@ fn find_skills_source(repo_dir: &Path) -> Option<PathBuf> {
     None
 }
 
+fn skills_staging_dir(target_dir: &Path) -> PathBuf {
+    let parent = target_dir
+        .parent()
+        .map(Path::to_path_buf)
+        .unwrap_or_else(|| PathBuf::from("."));
+    let target_name = target_dir
+        .file_name()
+        .and_then(|name| name.to_str())
+        .unwrap_or("skills");
+
+    parent.join(format!(
+        ".{}-installing-{}",
+        target_name,
+        uuid::Uuid::new_v4().simple()
+    ))
+}
+
+fn hidden_sibling_path(path: &Path, label: &str) -> PathBuf {
+    let parent = path
+        .parent()
+        .map(Path::to_path_buf)
+        .unwrap_or_else(|| PathBuf::from("."));
+    let name = path
+        .file_name()
+        .and_then(|name| name.to_str())
+        .unwrap_or("skill");
+
+    parent.join(format!(
+        ".{}-{}-{}",
+        name,
+        label,
+        uuid::Uuid::new_v4().simple()
+    ))
+}
+
+fn replace_dir_from_staging(staged: &Path, target: &Path) -> Result<(), String> {
+    let backup = hidden_sibling_path(target, "backup");
+    let had_existing = target.exists();
+
+    if had_existing {
+        std::fs::rename(target, &backup).map_err(|e| {
+            format!(
+                "Failed to prepare replacement for {}: {}",
+                target.display(),
+                e
+            )
+        })?;
+    }
+
+    match std::fs::rename(staged, target) {
+        Ok(()) => {
+            if had_existing {
+                let _ = std::fs::remove_dir_all(&backup);
+            }
+            Ok(())
+        }
+        Err(e) => {
+            let restore_error = if had_existing {
+                std::fs::rename(&backup, target)
+                    .err()
+                    .map(|restore| format!(" Restore also failed: {}", restore))
+            } else {
+                None
+            };
+
+            Err(format!(
+                "Failed to install {}: {}{}",
+                target.display(),
+                e,
+                restore_error.unwrap_or_default()
+            ))
+        }
+    }
+}
+
 /// Copy the skills directory from the downloaded repo to the target.
 fn copy_skills(repo_dir: &Path, target_dir: &Path) -> Result<usize, String> {
     let src = find_skills_source(repo_dir).ok_or_else(|| {
@@ -539,26 +1020,60 @@ fn copy_skills(repo_dir: &Path, target_dir: &Path) -> Result<usize, String> {
     std::fs::create_dir_all(target_dir)
         .map_err(|e| format!("Failed to create target dir: {}", e))?;
 
-    let mut count = 0;
-
     let mut skill_dirs = Vec::new();
     collect_skill_dirs(&src, &mut skill_dirs);
     skill_dirs.sort();
 
-    for entry_path in skill_dirs {
-        let Some(skill_name) = entry_path.file_name().and_then(|name| name.to_str()) else {
-            continue;
-        };
-        let target_skill = target_dir.join(skill_name);
-        if target_skill.exists() {
-            std::fs::remove_dir_all(&target_skill)
-                .map_err(|e| format!("Failed to replace {}: {}", target_skill.display(), e))?;
-        }
-        copy_dir_recursive(&entry_path, &target_skill)?;
-        count += 1;
+    if skill_dirs.is_empty() {
+        return Err("No skills found in downloaded repository".into());
     }
 
-    Ok(count)
+    let staging_dir = skills_staging_dir(target_dir);
+    std::fs::create_dir_all(&staging_dir)
+        .map_err(|e| format!("Failed to create staging dir: {}", e))?;
+
+    let mut staged_names = Vec::new();
+    let stage_result = (|| -> Result<(), String> {
+        for entry_path in &skill_dirs {
+            let Some(skill_name) = entry_path.file_name().and_then(|name| name.to_str()) else {
+                continue;
+            };
+
+            let staged_skill = staging_dir.join(skill_name);
+            copy_dir_recursive(entry_path, &staged_skill)?;
+            staged_names.push(skill_name.to_string());
+        }
+
+        Ok(())
+    })();
+
+    if let Err(e) = stage_result {
+        let _ = std::fs::remove_dir_all(&staging_dir);
+        return Err(e);
+    }
+
+    let replace_result = (|| -> Result<usize, String> {
+        let mut count = 0;
+        for skill_name in staged_names {
+            let staged_skill = staging_dir.join(&skill_name);
+            let target_skill = target_dir.join(&skill_name);
+
+            replace_dir_from_staging(&staged_skill, &target_skill).map_err(|e| {
+                format!(
+                    "Failed to replace {} with staged skill {}: {}",
+                    target_skill.display(),
+                    skill_name,
+                    e
+                )
+            })?;
+            count += 1;
+        }
+
+        Ok(count)
+    })();
+
+    let _ = std::fs::remove_dir_all(&staging_dir);
+    replace_result
 }
 
 /// Recursively copy a directory.
@@ -839,36 +1354,43 @@ async fn install_skills_to(
         msg
     })?;
 
-    // Download via tarball (faster, no git/git-lfs dependency)
-    emit_log(window, "Downloading skills...");
-    download_tarball(window, &tmp_dir).await.map_err(|e| {
-        emit_log(window, &format!("Download failed: {}", e));
-        e
-    })?;
-    emit_log(window, "Download complete");
+    let result = async {
+        // Download via tarball (faster, no git/git-lfs dependency)
+        emit_log(window, "Downloading skills...");
+        download_tarball(window, &tmp_dir).await.map_err(|e| {
+            emit_log(window, &format!("Download failed: {}", e));
+            e
+        })?;
+        emit_log(window, "Download complete");
 
-    let repo_dir = tmp_dir.join("repo");
+        let repo_dir = tmp_dir.join("repo");
 
-    // Copy skills to target directory
-    emit_log(window, "Copying skills...");
-    let count = copy_skills(&repo_dir, target).map_err(|e| {
-        emit_log(window, &format!("Copy failed: {}", e));
-        e
-    })?;
-    emit_log(window, &format!("Copied {} skills", count));
+        // Copy skills to target directory
+        emit_log(window, "Copying skills...");
+        let count = copy_skills(&repo_dir, target).map_err(|e| {
+            emit_log(window, &format!("Copy failed: {}", e));
+            e
+        })?;
+        emit_log(window, &format!("Copied {} skills", count));
 
-    // Clean up temp directory
-    let _ = std::fs::remove_dir_all(&tmp_dir);
-    emit_log(window, "Cleanup complete");
+        let target_str = target.to_string_lossy().to_string();
 
-    let target_str = target.to_string_lossy().to_string();
+        Ok(InstallResult {
+            success: true,
+            skills_installed: count,
+            target_dir: target_str.clone(),
+            message: format!("Successfully installed {} skills to {}", count, target_str),
+        })
+    }
+    .await;
 
-    Ok(InstallResult {
-        success: true,
-        skills_installed: count,
-        target_dir: target_str.clone(),
-        message: format!("Successfully installed {} skills to {}", count, target_str),
-    })
+    match std::fs::remove_dir_all(&tmp_dir) {
+        Ok(_) => emit_log(window, "Cleanup complete"),
+        Err(e) if tmp_dir.exists() => emit_log(window, &format!("Cleanup failed: {}", e)),
+        Err(_) => {}
+    }
+
+    result
 }
 
 #[tauri::command]
@@ -1010,27 +1532,44 @@ pub async fn get_skill_content(
 
     // Fallback: fetch from GitHub. The upstream project moved from
     // claude-scientific-skills/scientific-skills to scientific-agent-skills/skills.
-    let mut last_status = None;
+    let client = build_skills_http_client(SKILL_CONTENT_TIMEOUT_SECS, None)
+        .map_err(|e| format!("Failed to create GitHub client: {}", e))?;
+
+    let mut last_error = None;
     for base_url in RAW_SKILL_URLS {
-        let url = format!("{}/{}/SKILL.md", base_url, skill_folder);
-        let response = reqwest::get(&url)
-            .await
-            .map_err(|e| format!("Failed to fetch from GitHub: {}", e))?;
-
-        if response.status().is_success() {
-            return response
-                .text()
+        for skill_file in ["SKILL.md", "skill.md"] {
+            let url = format!("{}/{}/{}", base_url, skill_folder, skill_file);
+            let response = match client
+                .get(&url)
+                .header(reqwest::header::USER_AGENT, "ClaudePrism skills viewer")
+                .send()
                 .await
-                .map_err(|e| format!("Failed to read response: {}", e));
-        }
+            {
+                Ok(response) => response,
+                Err(e) => {
+                    last_error = Some(format!("{}: {}", url, e));
+                    continue;
+                }
+            };
 
-        last_status = Some(response.status().to_string());
+            if response.status().is_success() {
+                match response.text().await {
+                    Ok(text) => return Ok(text),
+                    Err(e) => {
+                        last_error = Some(format!("{}: failed to read response: {}", url, e));
+                        continue;
+                    }
+                }
+            }
+
+            last_error = Some(format!("{}: HTTP {}", url, response.status()));
+        }
     }
 
     Err(format!(
-        "Skill '{}' not found (HTTP {})",
+        "Skill '{}' not found. Last error: {}",
         skill_folder,
-        last_status.unwrap_or_else(|| "unknown".to_string())
+        last_error.unwrap_or_else(|| "unknown".to_string())
     ))
 }
 
@@ -1065,6 +1604,43 @@ mod tests {
         );
     }
 
+    #[test]
+    fn test_normalize_proxy_url_defaults_to_http() {
+        assert_eq!(
+            normalize_proxy_url("127.0.0.1:7890"),
+            Some("http://127.0.0.1:7890".to_string())
+        );
+        assert_eq!(
+            normalize_proxy_url("socks5://127.0.0.1:7891"),
+            Some("socks5://127.0.0.1:7891".to_string())
+        );
+        assert_eq!(normalize_proxy_url("   "), None);
+    }
+
+    #[cfg(target_os = "windows")]
+    #[test]
+    fn test_parse_windows_proxy_server_single_proxy() {
+        let rules = parse_windows_proxy_server("127.0.0.1:7890");
+        assert_eq!(rules.len(), 1);
+        assert_eq!(rules[0].kind, ProxyKind::All);
+        assert_eq!(rules[0].url, "http://127.0.0.1:7890");
+    }
+
+    #[cfg(target_os = "windows")]
+    #[test]
+    fn test_parse_windows_proxy_server_per_scheme_proxy() {
+        let rules = parse_windows_proxy_server(
+            "http=127.0.0.1:7890;https=127.0.0.1:7890;socks=127.0.0.1:7891",
+        );
+        assert_eq!(rules.len(), 3);
+        assert_eq!(rules[0].kind, ProxyKind::Http);
+        assert_eq!(rules[0].url, "http://127.0.0.1:7890");
+        assert_eq!(rules[1].kind, ProxyKind::Https);
+        assert_eq!(rules[1].url, "http://127.0.0.1:7890");
+        assert_eq!(rules[2].kind, ProxyKind::All);
+        assert_eq!(rules[2].url, "socks5://127.0.0.1:7891");
+    }
+
     #[test]
     fn test_skill_categories_count() {
         let cats = skill_categories();

apps/desktop/src/components/scientific-skills/scientific-skills-onboarding.tsx

@@ -78,8 +78,7 @@ export function ScientificSkillsOnboarding({
   const [installedSkills, setInstalledSkills] = useState<SkillInfo[]>([]);
   const [isUninstalling, setIsUninstalling] = useState(false);
   const [isImporting, setIsImporting] = useState(false);
-  const [confirmUninstallAllOpen, setConfirmUninstallAllOpen] =
-    useState(false);
+  const [confirmUninstallAllOpen, setConfirmUninstallAllOpen] = useState(false);
   const [deleteTarget, setDeleteTarget] = useState<SkillEntryData | null>(null);
   const [deletingSkillFolder, setDeletingSkillFolder] = useState<string | null>(
     null,
@@ -195,10 +194,7 @@ export function ScientificSkillsOnboarding({
             (line) => !line.startsWith("Preparing installer"),
           );
           if (hasBackendLog) return previous;
-          return [
-            ...previous,
-            "Waiting for the installer command to start...",
-          ];
+          return [...previous, "Waiting for the installer command to start..."];
         });
       }, 2500);
 
@@ -308,7 +304,7 @@ export function ScientificSkillsOnboarding({
   }, [checkStatus, deleteTarget]);
 
   // ─── Installing / Complete state ───
-  if (isInstalling || isComplete) {
+  if (isInstalling || isComplete || error) {
     return (
       <Dialog
         open
@@ -336,10 +332,16 @@ export function ScientificSkillsOnboarding({
             <DialogTitle className="flex items-center gap-2 text-sm">
               {isComplete ? (
                 <CheckCircle2Icon className="size-5 text-foreground" />
+              ) : error ? (
+                <AlertCircleIcon className="size-5 text-destructive" />
               ) : (
                 <FlaskConicalIcon className="size-5 text-muted-foreground" />
               )}
-              {isComplete ? "Installation Complete" : "Installing Skills"}
+              {isComplete
+                ? "Installation Complete"
+                : error
+                  ? "Installation Failed"
+                  : "Installing Skills"}
             </DialogTitle>
             {isComplete && (
               <DialogDescription>
@@ -370,10 +372,7 @@ export function ScientificSkillsOnboarding({
               <Button
                 variant="outline"
                 size="sm"
-                onClick={() => {
-                  setError(null);
-                  setIsInstalling(false);
-                }}
+                onClick={handleInstall}
                 className="gap-1.5"
               >
                 <RefreshCwIcon className="size-3.5" />
@@ -404,147 +403,149 @@ export function ScientificSkillsOnboarding({
           showCloseButton={false}
           className="flex h-[min(36rem,calc(100vh-6rem))] w-[min(56rem,calc(100vw-4rem))] max-w-none flex-col gap-0 overflow-hidden p-0 sm:max-w-none"
         >
-        {/* Header */}
-        <DialogHeader className="shrink-0 border-border border-b px-6 py-3">
-          <div className="flex items-center gap-4">
-            <div className="min-w-0 flex-1">
-              <DialogTitle className="text-sm">Skills</DialogTitle>
-              <DialogDescription className="mt-0.5 text-xs">
-                {totalSkills} skills across {displayCategories.length} groups -
-                install curated scientific skills or import a local Claude skill.
-                Curated set powered by{" "}
-                <a
-                  href="https://github.com/K-Dense-AI/scientific-agent-skills"
-                  target="_blank"
-                  rel="noopener noreferrer"
-                  className="inline-flex items-center gap-0.5 underline decoration-border underline-offset-2 hover:text-foreground"
-                >
-                  K-Dense
-                  <ExternalLinkIcon className="size-2.5" />
-                </a>
-              </DialogDescription>
-            </div>
-            <div className="flex shrink-0 items-center gap-2">
-              {isInstalled ? (
-                <>
-                  <Badge variant="secondary" className="gap-1 text-xs">
-                    <CheckCircle2Icon className="size-3" />
-                    {status?.skill_count} installed
-                  </Badge>
-                  <Button
-                    variant="outline"
-                    size="sm"
-                    onClick={handleInstall}
-                    className="gap-1.5"
+          {/* Header */}
+          <DialogHeader className="shrink-0 border-border border-b px-6 py-3">
+            <div className="flex items-center gap-4">
+              <div className="min-w-0 flex-1">
+                <DialogTitle className="text-sm">Skills</DialogTitle>
+                <DialogDescription className="mt-0.5 text-xs">
+                  {totalSkills} skills across {displayCategories.length} groups
+                  - install curated scientific skills or import a local Claude
+                  skill. Curated set powered by{" "}
+                  <a
+                    href="https://github.com/K-Dense-AI/scientific-agent-skills"
+                    target="_blank"
+                    rel="noopener noreferrer"
+                    className="inline-flex items-center gap-0.5 underline decoration-border underline-offset-2 hover:text-foreground"
                   >
-                    <RefreshCwIcon className="size-3.5" />
-                    Update
-                  </Button>
-                  <Button
-                    variant="outline"
-                    size="sm"
-                    onClick={() => setConfirmUninstallAllOpen(true)}
-                    disabled={isUninstalling}
-                    className="gap-1.5 text-destructive hover:text-destructive"
-                  >
-                    {isUninstalling ? (
-                      <Loader2Icon className="size-3.5 animate-spin" />
-                    ) : (
-                      <Trash2Icon className="size-3.5" />
-                    )}
-                    Uninstall
-                  </Button>
-                </>
-              ) : (
-                <Button size="sm" onClick={handleInstall} className="gap-1.5">
-                  <DownloadIcon className="size-3.5" />
-                  Install All
-                </Button>
-              )}
-              <Button
-                variant="outline"
-                size="sm"
-                onClick={handleImportSkill}
-                disabled={isImporting || isInstalling || isUninstalling}
-                className="gap-1.5 text-green-600 hover:text-green-700 dark:text-green-400 dark:hover:text-green-300"
-              >
-                {isImporting ? (
-                  <Loader2Icon className="size-3.5 animate-spin" />
-                ) : (
-                  <FolderPlusIcon className="size-3.5" />
-                )}
-                Import Skill
-              </Button>
-            </div>
-          </div>
-        </DialogHeader>
-
-        {/* Body — sidebar + detail */}
-        <div className="flex flex-1 overflow-hidden">
-          {/* Category sidebar */}
-          <nav className="w-64 max-w-64 shrink-0 overflow-hidden border-border border-r">
-            <ScrollArea className="h-full w-full overflow-hidden [&_[data-slot=scroll-area-scrollbar]]:hidden">
-              <div className="box-border flex w-full min-w-0 flex-col gap-0.5 overflow-x-hidden p-2">
-                {displayCategories.map((cat) => {
-                  const Icon = ICON_MAP[cat.icon] || FlaskConicalIcon;
-                  const isActive = selectedId === cat.id;
-                  return (
-                    <button
-                      key={cat.id}
-                      onClick={() => setSelectedId(cat.id)}
-                      className={cn(
-                        "box-border grid w-full max-w-full min-w-0 grid-cols-[1rem_minmax(0,1fr)] items-center gap-2.5 overflow-hidden rounded-lg px-3 py-2 text-left text-sm transition-colors",
-                        isActive
-                          ? "bg-accent font-medium text-accent-foreground"
-                          : "text-muted-foreground hover:bg-accent/50 hover:text-foreground",
-                      )}
-                      title={cat.name}
-                    >
-                      <Icon className="size-4 shrink-0" />
-                      <span className="block min-w-0 truncate">{cat.name}</span>
-                    </button>
-                  );
-                })}
+                    K-Dense
+                    <ExternalLinkIcon className="size-2.5" />
+                  </a>
+                </DialogDescription>
               </div>
-            </ScrollArea>
-          </nav>
+              <div className="flex shrink-0 items-center gap-2">
+                {isInstalled ? (
+                  <>
+                    <Badge variant="secondary" className="gap-1 text-xs">
+                      <CheckCircle2Icon className="size-3" />
+                      {status?.skill_count} installed
+                    </Badge>
+                    <Button
+                      variant="outline"
+                      size="sm"
+                      onClick={handleInstall}
+                      className="gap-1.5"
+                    >
+                      <RefreshCwIcon className="size-3.5" />
+                      Update
+                    </Button>
+                    <Button
+                      variant="outline"
+                      size="sm"
+                      onClick={() => setConfirmUninstallAllOpen(true)}
+                      disabled={isUninstalling}
+                      className="gap-1.5 text-destructive hover:text-destructive"
+                    >
+                      {isUninstalling ? (
+                        <Loader2Icon className="size-3.5 animate-spin" />
+                      ) : (
+                        <Trash2Icon className="size-3.5" />
+                      )}
+                      Uninstall
+                    </Button>
+                  </>
+                ) : (
+                  <Button size="sm" onClick={handleInstall} className="gap-1.5">
+                    <DownloadIcon className="size-3.5" />
+                    Install All
+                  </Button>
+                )}
+                <Button
+                  variant="outline"
+                  size="sm"
+                  onClick={handleImportSkill}
+                  disabled={isImporting || isInstalling || isUninstalling}
+                  className="gap-1.5 text-green-600 hover:text-green-700 dark:text-green-400 dark:hover:text-green-300"
+                >
+                  {isImporting ? (
+                    <Loader2Icon className="size-3.5 animate-spin" />
+                  ) : (
+                    <FolderPlusIcon className="size-3.5" />
+                  )}
+                  Import Skill
+                </Button>
+              </div>
+            </div>
+          </DialogHeader>
 
-          {/* Detail panel */}
-          <div className="flex flex-1 flex-col overflow-hidden">
-            {selected ? (
-              <ScrollArea className="flex-1">
-                <div className="p-6">
-                  <CategoryDetail
-                    category={selected}
-                    isInstalled={isInstalled}
-                    installedSkillFolders={installedSkillFolders}
-                    deletingSkillFolder={deletingSkillFolder}
-                    onDeleteSkill={setDeleteTarget}
-                  />
+          {/* Body — sidebar + detail */}
+          <div className="flex flex-1 overflow-hidden">
+            {/* Category sidebar */}
+            <nav className="w-64 max-w-64 shrink-0 overflow-hidden border-border border-r">
+              <ScrollArea className="h-full w-full overflow-hidden [&_[data-slot=scroll-area-scrollbar]]:hidden">
+                <div className="box-border flex w-full min-w-0 flex-col gap-0.5 overflow-x-hidden p-2">
+                  {displayCategories.map((cat) => {
+                    const Icon = ICON_MAP[cat.icon] || FlaskConicalIcon;
+                    const isActive = selectedId === cat.id;
+                    return (
+                      <button
+                        key={cat.id}
+                        onClick={() => setSelectedId(cat.id)}
+                        className={cn(
+                          "box-border grid w-full min-w-0 max-w-full grid-cols-[1rem_minmax(0,1fr)] items-center gap-2.5 overflow-hidden rounded-lg px-3 py-2 text-left text-sm transition-colors",
+                          isActive
+                            ? "bg-accent font-medium text-accent-foreground"
+                            : "text-muted-foreground hover:bg-accent/50 hover:text-foreground",
+                        )}
+                        title={cat.name}
+                      >
+                        <Icon className="size-4 shrink-0" />
+                        <span className="block min-w-0 truncate">
+                          {cat.name}
+                        </span>
+                      </button>
+                    );
+                  })}
                 </div>
               </ScrollArea>
-            ) : (
-              <div className="flex flex-1 items-center justify-center text-muted-foreground text-sm">
-                Select a category
-              </div>
-            )}
-          </div>
-        </div>
+            </nav>
 
-        {/* Footer */}
-        <div className="flex shrink-0 items-center justify-between border-border border-t bg-muted/20 px-6 py-2.5">
-          <p className="font-mono text-[11px] text-muted-foreground/60">
-            {status?.location ?? "~/.claude/skills/"}
-          </p>
-          <Button
-            variant="ghost"
-            size="sm"
-            onClick={onClose}
-            className="text-muted-foreground"
-          >
-            Close
-          </Button>
-        </div>
+            {/* Detail panel */}
+            <div className="flex flex-1 flex-col overflow-hidden">
+              {selected ? (
+                <ScrollArea className="flex-1">
+                  <div className="p-6">
+                    <CategoryDetail
+                      category={selected}
+                      isInstalled={isInstalled}
+                      installedSkillFolders={installedSkillFolders}
+                      deletingSkillFolder={deletingSkillFolder}
+                      onDeleteSkill={setDeleteTarget}
+                    />
+                  </div>
+                </ScrollArea>
+              ) : (
+                <div className="flex flex-1 items-center justify-center text-muted-foreground text-sm">
+                  Select a category
+                </div>
+              )}
+            </div>
+          </div>
+
+          {/* Footer */}
+          <div className="flex shrink-0 items-center justify-between border-border border-t bg-muted/20 px-6 py-2.5">
+            <p className="font-mono text-[11px] text-muted-foreground/60">
+              {status?.location ?? "~/.claude/skills/"}
+            </p>
+            <Button
+              variant="ghost"
+              size="sm"
+              onClick={onClose}
+              className="text-muted-foreground"
+            >
+              Close
+            </Button>
+          </div>
         </DialogContent>
       </Dialog>
 
@@ -558,8 +559,8 @@ export function ScientificSkillsOnboarding({
           <DialogHeader>
             <DialogTitle>Delete Skill</DialogTitle>
             <DialogDescription>
-              Delete {deleteTarget?.name ?? "this skill"} from
-              ~/.claude/skills. This cannot be undone.
+              Delete {deleteTarget?.name ?? "this skill"} from ~/.claude/skills.
+              This cannot be undone.
             </DialogDescription>
           </DialogHeader>
           <div className="rounded-lg border border-border/60 bg-muted/30 px-3 py-2 font-mono text-muted-foreground text-xs">
@@ -823,7 +824,7 @@ function CategoryDetail({
                       event.stopPropagation();
                       onDeleteSkill(skill);
                     }}
-                    className="mr-1 flex size-7 shrink-0 items-center justify-center rounded-md text-muted-foreground opacity-70 transition-colors hover:bg-destructive/10 hover:text-destructive group-hover:opacity-100 disabled:opacity-50"
+                    className="mr-1 flex size-7 shrink-0 items-center justify-center rounded-md text-muted-foreground opacity-70 transition-colors hover:bg-destructive/10 hover:text-destructive disabled:opacity-50 group-hover:opacity-100"
                   >
                     {isDeleting ? (
                       <Loader2Icon className="size-3.5 animate-spin" />