System addon does not override app-profile addon
In #25013 (moved), torbutton was added as a system addon in TBA, but it seems like the app continues using the version in the profile after the app upgrade. I toggled extensions.logging.enabled, these are some of the log entries.
torbutton is copied into the app's writable storage, but it isn't installed. It also doesn't find the new preferences.json file.
11-28 01:23:40.492 8476 8493 D GeckoProfile: Found profile dir.
11-28 01:23:40.539 8476 8476 D StrictMode: at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:858)
11-28 01:23:40.546 8476 8493 D PostUpdateHandler: Build ID changed since last start: '20181128012042', '20181128011144'
11-28 01:23:40.546 8476 8493 D PostUpdateHandler: Copying system add-ons from APK to dataDir
11-28 01:23:40.548 8476 8493 D PostUpdateHandler: Copying 'features/torbutton@torproject.org.xpi' from APK to dataDir
11-28 01:23:40.552 8476 8493 D PostUpdateHandler: Creating /data/user/0/org.torproject.torbrowser_alpha/features
11-28 01:23:40.558 8476 8493 D GeckoSessInfo: Recording start of session: 1543368220513
11-28 01:23:40.558 8476 8493 D GeckoDistribution: Getting file from distribution.
11-28 01:23:40.558 8476 8493 E GeckoDistribution: Distribution directory exists, but no file named preferences.json
11-28 01:23:40.558 8476 8493 D GeckoSearchEngineManager: Found default engine name in SharedPreferences: DuckDuckGo
11-28 01:23:40.558 8476 8493 D GeckoDistribution: Getting file from distribution.
11-28 01:23:43.111 8476 8496 I Gecko : 1543368223110 addons.manager DEBUG Loaded provider scope for re[/gre/modules/addons/XPIProvider.jsm:](/gre/modules/addons/XPIProvider.jsm:) ["XPIProvider", "XPIInternal"]
11-28 01:23:43.114 8476 8496 I Gecko : 1543368223114 addons.manager DEBUG Loaded provider scope for re[/gre/modules/LightweightThemeManager.jsm:](/gre/modules/LightweightThemeManager.jsm:) ["LightweightThemeManager"]
11-28 01:23:43.137 8476 8496 I Gecko : 1543368223136 addons.manager DEBUG Loaded provider scope for re[/gre/modules/addons/GMPProvider.jsm](/gre/modules/addons/GMPProvider.jsm)
11-28 01:23:43.137 8476 8496 I Gecko : 1543368223137 addons.manager DEBUG Starting provider: XPIProvider
11-28 01:23:43.137 8476 8496 I Gecko : 1543368223137 addons.xpi DEBUG startup
11-28 01:23:43.139 8476 8496 I Gecko : 1543368223139 addons.xpi INFO SystemAddonInstallLocation directory is missing
11-28 01:23:43.140 8476 8496 I Gecko : 1543368223139 addons.xpi DEBUG checkForChanges
11-28 01:23:43.141 8476 8496 I Gecko : 1543368223140 addons.xpi DEBUG Loaded add-on state: {"app-profile":{"addons":{"{73a6fe31-595d-460b-a920-fcc0f8843232}":{"enabled":true,"lastModifiedTime":1543367768000,"path":"{73a6fe31-595d-460b-a920-fcc0f8843232}.xpi","signedState":2,"version":"10.2.0","type":"webextension","bootstrapped":true,"dependencies":[],"runInSafeMode":false,"hasEmbeddedWebExtension":false},"https-everywhere-eff@eff.org":{"enabled":true,"lastModifiedTime":1543367678000,"path":"https-everywhere-eff@eff.org.xpi","signedState":2,"version":"2018.4.11","type":"webextension","bootstrapped":true,"dependencies":[],"runInSafeMode":false,"hasEmbeddedWebExtension":false},"torbutton@torproject.org":{"enabled":true,"lastModifiedTime":1543367720000,"path":"torbutton@torproject.org.xpi","version":"2.1.1"}},"path":"/data/user/0/org.torproject.torbrowser_alpha/files/mozilla/rb02if1q.default/extensions"}}
11-28 01:23:43.142 8476 8496 I Gecko : 1543368223142 addons.xpi INFO Mapping {73a6fe31-595d-460b-a920-fcc0f8843232} to /data/user/0/org.torproject.torbrowser_alpha/files/mozilla/rb02if1q.default/extensions/{73a6fe31-595d-460b-a920-fcc0f8843232}.xpi
11-28 01:23:43.143 8476 8496 I Gecko : 1543368223143 addons.xpi INFO Mapping https-everywhere-eff@eff.org to /data/user/0/org.torproject.torbrowser_alpha/files/mozilla/rb02if1q.default/extensions/https-everywhere-eff@eff.org.xpi
11-28 01:23:43.143 8476 8496 I Gecko : 1543368223143 addons.xpi INFO Mapping torbutton@torproject.org to /data/user/0/org.torproject.torbrowser_alpha/files/mozilla/rb02if1q.default/extensions/torbutton@torproject.org.xpi
11-28 01:23:43.144 8476 8496 I Gecko : 1543368223144 addons.xpi INFO Mapping {73a6fe31-595d-460b-a920-fcc0f8843232} to /data/user/0/org.torproject.torbrowser_alpha/files/mozilla/rb02if1q.default/extensions/{73a6fe31-595d-460b-a920-fcc0f8843232}.xpi
11-28 01:23:43.144 8476 8496 I Gecko : 1543368223144 addons.xpi INFO Mapping https-everywhere-eff@eff.org to /data/user/0/org.torproject.torbrowser_alpha/files/mozilla/rb02if1q.default/extensions/https-everywhere-eff@eff.org.xpi
11-28 01:23:43.144 8476 8496 I Gecko : 1543368223144 addons.xpi INFO Mapping torbutton@torproject.org to /data/user/0/org.torproject.torbrowser_alpha/files/mozilla/rb02if1q.default/extensions/torbutton@torproject.org.xpi
11-28 01:23:43.145 8476 8496 I Gecko : 1543368223145 addons.xpi DEBUG Existing add-on {73a6fe31-595d-460b-a920-fcc0f8843232} in app-profile
11-28 01:23:43.145 8476 8496 I Gecko : 1543368223145 addons.xpi DEBUG Existing add-on https-everywhere-eff@eff.org in app-profile
11-28 01:23:43.146 8476 8496 I Gecko : 1543368223146 addons.xpi DEBUG Existing add-on torbutton@torproject.org in app-profile
11-28 01:23:43.148 8476 8496 I Gecko : 1543368223147 addons.xpi WARN List of valid built-in add-ons could not be parsed.: [Exception... "Component returned failure code: 0x80520001 (NS_ERROR_FILE_UNRECOGNIZED_PATH) [nsIXPCComponents_Utils.readUTF8URI]" nsresult: "0x80520001 (NS_ERROR_FILE_UNRECOGNIZED_PATH)" location: "JS frame :: re[/gre/modules/addons/XPIProvider.jsm](/gre/modules/addons/XPIProvider.jsm) :: _readAddons :: line 6484" data: no] Stack trace: _readAddons()@re[/gre/modules/addons/XPIProvider.jsm:6484](/gre/modules/addons/XPIProvider.jsm:6484)
11-28 01:23:43.148 8476 8496 I Gecko : getAddonLocations()@re[/gre/modules/addons/XPIProvider.jsm:6145](/gre/modules/addons/XPIProvider.jsm:6145)
11-28 01:23:43.148 8476 8496 I Gecko : getInstallState()@re[/gre/modules/addons/XPIProvider.jsm:1601](/gre/modules/addons/XPIProvider.jsm:1601)
11-28 01:23:43.148 8476 8496 I Gecko : checkForChanges()@re[/gre/modules/addons/XPIProvider.jsm:3295](/gre/modules/addons/XPIProvider.jsm:3295)
11-28 01:23:43.148 8476 8496 I Gecko : startup()@re[/gre/modules/addons/XPIProvider.jsm:2203](/gre/modules/addons/XPIProvider.jsm:2203)
11-28 01:23:43.148 8476 8496 I Gecko : callProvider()@re[/gre/modules/AddonManager.jsm:258](/gre/modules/AddonManager.jsm:258)
11-28 01:23:43.148 8476 8496 I Gecko : _startProvider()@re[/gre/modules/AddonManager.jsm:733](/gre/modules/AddonManager.jsm:733)
11-28 01:23:43.148 8476 8496 I Gecko : startup()@re[/gre/modules/AddonManager.jsm:921](/gre/modules/AddonManager.jsm:921)
11-28 01:23:43.148 8476 8496 I Gecko : startup()@re[/gre/modules/AddonManager.jsm:3005](/gre/modules/AddonManager.jsm:3005)
11-28 01:23:43.148 8476 8496 I Gecko : observe()@jar:jar:file:///data/app/org.torproject.torbrowser_alp
11-28 01:23:43.149 8476 8496 I Gecko : 1543368223149 addons.xpi DEBUG getInstallState changed: false, state: {}
11-28 01:23:43.150 8476 8496 I Gecko : 1543368223150 addons.xpi INFO SystemAddonInstallLocation directory is missing
11-28 01:23:43.154 8476 8496 I Gecko : 1543368223154 addons.xpi DEBUG No changes found
11-28 01:23:43.155 8476 8496 I Gecko : 1543368223155 addons.xpi DEBUG Loading bootstrap scope from /data/user/0/org.torproject.torbrowser_alpha/files/mozilla/rb02if1q.default/extensions/https-everywhere-eff@eff.org.xpi
11-28 01:23:43.179 8476 8496 I Gecko : 1543368223179 addons.xpi DEBUG Calling bootstrap method startup on https-everywhere-eff@eff.org version 2018.4.11
11-28 01:23:43.183 8476 8496 I Gecko : 1543368223183 addons.xpi DEBUG Loading bootstrap scope from /data/user/0/org.torproject.torbrowser_alpha/files/mozilla/rb02if1q.default/extensions/{73a6fe31-595d-460b-a920-fcc0f8843232}.xpi
11-28 01:23:43.184 8476 8496 I Gecko : 1543368223184 addons.xpi DEBUG Calling bootstrap method startup on {73a6fe31-595d-460b-a920-fcc0f8843232} version 10.2.0
11-28 01:23:43.187 8476 8496 I Gecko : 1543368223187 addons.manager DEBUG Registering shutdown blocker for XPIProvider
11-28 01:23:43.187 8476 8496 I Gecko : 1543368223187 addons.manager DEBUG Provider finished startup: XPIProvider
11-28 01:23:43.795 8476 8496 I Gecko : 1543368223795 addons.xpi-utils DEBUG Starting async load of XPI database /data/user/0/org.torproject.torbrowser_alpha/files/mozilla/rb02if1q.default/extensions.json
11-28 01:23:44.104 8476 8496 I Gecko : 1543368224104 addons.xpi-utils DEBUG Async JSON file read took 0 MS
11-28 01:23:44.104 8476 8496 I Gecko : 1543368224104 addons.xpi-utils DEBUG Finished async read of XPI database, parsing...
11-28 01:23:44.107 8476 8496 I Gecko : 1543368224107 addons.xpi-utils DEBUG Successfully read XPI database
11-28 01:23:44.124 8476 8496 D GeckoDistribution: Custom distribution directory not found.